Starting phenix.real_space_refine on Mon Dec 30 08:48:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ce0_45489/12_2024/9ce0_45489_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ce0_45489/12_2024/9ce0_45489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ce0_45489/12_2024/9ce0_45489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ce0_45489/12_2024/9ce0_45489.map" model { file = "/net/cci-nas-00/data/ceres_data/9ce0_45489/12_2024/9ce0_45489_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ce0_45489/12_2024/9ce0_45489_neut.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 2 7.16 5 S 66 5.16 5 C 7957 2.51 5 N 2188 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12551 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 787, 6257 Classifications: {'peptide': 787} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 33, 'TRANS': 750} Chain: "B" Number of atoms: 6204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6204 Classifications: {'peptide': 781} Link IDs: {'PTRANS': 35, 'TRANS': 745} Chain breaks: 1 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'HEM': 1, 'OXY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.74, per 1000 atoms: 0.62 Number of scatterers: 12551 At special positions: 0 Unit cell: (93.6383, 103.325, 195.349, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 2 26.01 S 66 16.00 O 2338 8.00 N 2188 7.00 C 7957 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2956 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 51.0% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 3.802A pdb=" N ALA A 25 " --> pdb=" O ILE A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.810A pdb=" N VAL A 60 " --> pdb=" O LYS A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.929A pdb=" N MET A 67 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.647A pdb=" N TYR A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 119 through 123 Processing helix chain 'A' and resid 133 through 152 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 180 through 185 Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 200 through 212 removed outlier: 4.202A pdb=" N ILE A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 275 Processing helix chain 'A' and resid 278 through 294 Processing helix chain 'A' and resid 352 through 383 Processing helix chain 'A' and resid 394 through 409 Processing helix chain 'A' and resid 421 through 429 Processing helix chain 'A' and resid 430 through 449 removed outlier: 4.219A pdb=" N GLN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 440 " --> pdb=" O GLN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 512 through 531 Processing helix chain 'A' and resid 542 through 563 removed outlier: 3.627A pdb=" N ARG A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 609 Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 611 through 634 Processing helix chain 'A' and resid 645 through 648 Processing helix chain 'A' and resid 650 through 652 No H-bonds generated for 'chain 'A' and resid 650 through 652' Processing helix chain 'A' and resid 653 through 665 removed outlier: 4.265A pdb=" N ALA A 661 " --> pdb=" O GLN A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 699 Processing helix chain 'A' and resid 710 through 720 removed outlier: 3.758A pdb=" N LEU A 720 " --> pdb=" O ARG A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 736 removed outlier: 3.813A pdb=" N ARG A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 736 " --> pdb=" O VAL A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 756 removed outlier: 3.615A pdb=" N LEU A 742 " --> pdb=" O GLU A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 777 Processing helix chain 'A' and resid 794 through 803 removed outlier: 3.859A pdb=" N SER A 800 " --> pdb=" O PRO A 796 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 76 through 88 removed outlier: 3.621A pdb=" N GLY B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 134 through 153 Processing helix chain 'B' and resid 170 through 178 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 188 through 193 Processing helix chain 'B' and resid 201 through 210 removed outlier: 4.054A pdb=" N ARG B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 276 Processing helix chain 'B' and resid 278 through 294 Processing helix chain 'B' and resid 352 through 377 Processing helix chain 'B' and resid 394 through 408 removed outlier: 3.686A pdb=" N LYS B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 447 removed outlier: 4.142A pdb=" N VAL B 425 " --> pdb=" O HIS B 421 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N TYR B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N ALA B 432 " --> pdb=" O SER B 428 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TRP B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 486 removed outlier: 3.755A pdb=" N VAL B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 531 Processing helix chain 'B' and resid 539 through 562 Processing helix chain 'B' and resid 598 through 610 Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 611 through 632 Processing helix chain 'B' and resid 643 through 648 Processing helix chain 'B' and resid 650 through 654 removed outlier: 3.921A pdb=" N GLN B 653 " --> pdb=" O ARG B 650 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LEU B 654 " --> pdb=" O SER B 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 650 through 654' Processing helix chain 'B' and resid 655 through 665 removed outlier: 4.914A pdb=" N ALA B 661 " --> pdb=" O GLN B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 683 Processing helix chain 'B' and resid 686 through 699 removed outlier: 3.706A pdb=" N LYS B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 Processing helix chain 'B' and resid 728 through 733 Processing helix chain 'B' and resid 738 through 755 Processing helix chain 'B' and resid 766 through 776 Processing helix chain 'B' and resid 794 through 802 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 36 Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 168 removed outlier: 3.764A pdb=" N GLN A 168 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 314 removed outlier: 6.615A pdb=" N LEU A 301 " --> pdb=" O TRP A 312 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER A 314 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL A 299 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN A 343 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 339 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 331 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE A 341 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ALA A 329 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A 343 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TRP A 327 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS A 345 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLN A 325 " --> pdb=" O LYS A 345 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 459 removed outlier: 5.507A pdb=" N LEU A 455 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 466 " --> pdb=" O LEU A 455 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG A 457 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 464 " --> pdb=" O ARG A 457 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 459 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 490 through 492 Processing sheet with id=AA6, first strand: chain 'A' and resid 566 through 573 removed outlier: 4.453A pdb=" N TRP A 589 " --> pdb=" O VAL A 597 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 566 through 573 removed outlier: 4.652A pdb=" N ASN A 643 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ALA A 587 " --> pdb=" O ASN A 643 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 675 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 701 " --> pdb=" O LEU A 672 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 702 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LYS A 726 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 704 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE A 725 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU A 762 " --> pdb=" O ILE A 725 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE A 727 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL A 764 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N GLN A 782 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA A 761 " --> pdb=" O GLN A 782 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45 removed outlier: 6.673A pdb=" N LEU B 35 " --> pdb=" O MET B 43 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N PHE B 45 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA B 33 " --> pdb=" O PHE B 45 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 32 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 166 through 168 removed outlier: 6.055A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 308 through 314 removed outlier: 6.714A pdb=" N LEU B 301 " --> pdb=" O TRP B 312 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 314 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL B 299 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA B 339 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE B 331 " --> pdb=" O ALA B 339 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE B 341 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 329 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN B 343 " --> pdb=" O TRP B 327 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TRP B 327 " --> pdb=" O GLN B 343 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LYS B 345 " --> pdb=" O GLN B 325 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN B 325 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 454 through 459 removed outlier: 7.109A pdb=" N GLN B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 672 through 674 removed outlier: 6.344A pdb=" N LEU B 640 " --> pdb=" O THR B 673 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER B 641 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE B 583 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN B 572 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ILE B 583 " --> pdb=" O GLN B 570 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N GLN B 570 " --> pdb=" O ILE B 583 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA B 585 " --> pdb=" O VAL B 568 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 568 " --> pdb=" O ALA B 585 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA B 587 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LYS B 566 " --> pdb=" O ALA B 587 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL B 759 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 725 " --> pdb=" O VAL B 760 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 590 through 591 696 hydrogen bonds defined for protein. 1998 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: 4.95 Time building geometry restraints manager: 4.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 4943 1.38 - 1.56: 7750 1.56 - 1.73: 0 1.73 - 1.91: 116 1.91 - 2.08: 8 Bond restraints: 12817 Sorted by residual: bond pdb=" CA SER A 600 " pdb=" C SER A 600 " ideal model delta sigma weight residual 1.522 1.475 0.047 1.45e-02 4.76e+03 1.03e+01 bond pdb=" N PHE B 386 " pdb=" CA PHE B 386 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.13e-02 7.83e+03 6.19e+00 bond pdb=" N ILE B 384 " pdb=" CA ILE B 384 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.90e-02 2.77e+03 3.60e+00 bond pdb=" N GLN B 385 " pdb=" CA GLN B 385 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.58e-02 4.01e+03 3.56e+00 bond pdb=" C ASP B 387 " pdb=" N PRO B 388 " ideal model delta sigma weight residual 1.334 1.347 -0.013 8.40e-03 1.42e+04 2.37e+00 ... (remaining 12812 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 16472 1.45 - 2.90: 803 2.90 - 4.36: 102 4.36 - 5.81: 8 5.81 - 7.26: 3 Bond angle restraints: 17388 Sorted by residual: angle pdb=" N ILE A 148 " pdb=" CA ILE A 148 " pdb=" C ILE A 148 " ideal model delta sigma weight residual 110.72 106.18 4.54 1.01e+00 9.80e-01 2.02e+01 angle pdb=" N ARG A 779 " pdb=" CA ARG A 779 " pdb=" CB ARG A 779 " ideal model delta sigma weight residual 114.17 109.61 4.56 1.14e+00 7.69e-01 1.60e+01 angle pdb=" C GLU B 793 " pdb=" N GLU B 794 " pdb=" CA GLU B 794 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.39e+01 angle pdb=" N GLN B 385 " pdb=" CA GLN B 385 " pdb=" C GLN B 385 " ideal model delta sigma weight residual 113.40 108.14 5.26 1.47e+00 4.63e-01 1.28e+01 angle pdb=" N ASP A 151 " pdb=" CA ASP A 151 " pdb=" C ASP A 151 " ideal model delta sigma weight residual 111.28 107.61 3.67 1.09e+00 8.42e-01 1.13e+01 ... (remaining 17383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 6911 17.75 - 35.50: 648 35.50 - 53.25: 127 53.25 - 71.00: 41 71.00 - 88.75: 17 Dihedral angle restraints: 7744 sinusoidal: 3191 harmonic: 4553 Sorted by residual: dihedral pdb=" CA GLN B 657 " pdb=" C GLN B 657 " pdb=" N VAL B 658 " pdb=" CA VAL B 658 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY A 227 " pdb=" C GLY A 227 " pdb=" N GLU A 228 " pdb=" CA GLU A 228 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA LEU A 720 " pdb=" C LEU A 720 " pdb=" N PRO A 721 " pdb=" CA PRO A 721 " ideal model delta harmonic sigma weight residual 180.00 -154.42 -25.58 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 7741 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1405 0.040 - 0.080: 363 0.080 - 0.120: 137 0.120 - 0.160: 16 0.160 - 0.200: 1 Chirality restraints: 1922 Sorted by residual: chirality pdb=" CA ILE B 384 " pdb=" N ILE B 384 " pdb=" C ILE B 384 " pdb=" CB ILE B 384 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CA ILE A 331 " pdb=" N ILE A 331 " pdb=" C ILE A 331 " pdb=" CB ILE A 331 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ILE A 69 " pdb=" N ILE A 69 " pdb=" C ILE A 69 " pdb=" CB ILE A 69 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1919 not shown) Planarity restraints: 2261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 155 " -0.037 5.00e-02 4.00e+02 5.58e-02 4.98e+00 pdb=" N PRO A 156 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 156 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 156 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 266 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.93e+00 pdb=" C GLU B 266 " -0.038 2.00e-02 2.50e+03 pdb=" O GLU B 266 " 0.014 2.00e-02 2.50e+03 pdb=" N GLY B 267 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 144 " -0.011 2.00e-02 2.50e+03 2.14e-02 4.57e+00 pdb=" C ARG B 144 " 0.037 2.00e-02 2.50e+03 pdb=" O ARG B 144 " -0.014 2.00e-02 2.50e+03 pdb=" N GLN B 145 " -0.012 2.00e-02 2.50e+03 ... (remaining 2258 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 184 2.52 - 3.12: 10812 3.12 - 3.71: 20858 3.71 - 4.31: 27856 4.31 - 4.90: 45103 Nonbonded interactions: 104813 Sorted by model distance: nonbonded pdb=" O LYS A 140 " pdb=" OG1 THR A 143 " model vdw 1.931 3.040 nonbonded pdb=" O ALA A 272 " pdb=" OG SER A 275 " model vdw 1.963 3.040 nonbonded pdb=" O ASN A 84 " pdb=" OH TYR A 126 " model vdw 1.979 3.040 nonbonded pdb=" OG SER B 632 " pdb=" OE1 GLN B 633 " model vdw 1.997 3.040 nonbonded pdb=" O GLY B 708 " pdb=" OG1 THR B 709 " model vdw 2.048 3.040 ... (remaining 104808 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' and (resid 20 through 377 or resid 384 through 806 or resid 901 throu \ gh 902)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 31.990 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12817 Z= 0.271 Angle : 0.693 7.261 17388 Z= 0.460 Chirality : 0.042 0.200 1922 Planarity : 0.006 0.069 2261 Dihedral : 15.095 88.749 4788 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.27 % Favored : 93.60 % Rotamer: Outliers : 0.15 % Allowed : 9.12 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % 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: -1.00 (0.21), residues: 1562 helix: 0.30 (0.20), residues: 713 sheet: -0.96 (0.29), residues: 322 loop : -1.66 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 665 HIS 0.005 0.001 HIS A 365 PHE 0.022 0.002 PHE A 602 TYR 0.018 0.001 TYR B 454 ARG 0.004 0.001 ARG B 164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 138 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: -0.0135 (ptm) cc_final: -0.0391 (ptt) REVERT: A 43 MET cc_start: 0.2565 (mpp) cc_final: 0.2218 (mpp) REVERT: B 416 LEU cc_start: 0.9074 (tp) cc_final: 0.8351 (tp) outliers start: 2 outliers final: 0 residues processed: 140 average time/residue: 0.2940 time to fit residues: 57.8509 Evaluate side-chains 88 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 122 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 GLN ** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 HIS B 139 GLN B 142 GLN B 217 GLN B 248 ASN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12817 Z= 0.234 Angle : 0.748 8.918 17388 Z= 0.379 Chirality : 0.047 0.198 1922 Planarity : 0.006 0.062 2261 Dihedral : 6.400 76.350 1707 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.67 % Favored : 95.20 % Rotamer: Outliers : 1.54 % Allowed : 13.16 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1562 helix: 0.36 (0.19), residues: 719 sheet: -0.76 (0.28), residues: 340 loop : -1.34 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 589 HIS 0.007 0.001 HIS A 77 PHE 0.024 0.002 PHE B 602 TYR 0.016 0.002 TYR B 179 ARG 0.005 0.001 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.2823 (mpp) cc_final: 0.1690 (mmt) REVERT: A 113 PHE cc_start: 0.5446 (t80) cc_final: 0.4817 (t80) REVERT: B 31 MET cc_start: 0.1871 (mmp) cc_final: 0.1412 (mmp) REVERT: B 253 PHE cc_start: 0.7369 (m-80) cc_final: 0.7132 (m-10) REVERT: B 698 MET cc_start: 0.8344 (mtt) cc_final: 0.8136 (mtp) outliers start: 21 outliers final: 5 residues processed: 106 average time/residue: 0.2561 time to fit residues: 40.0498 Evaluate side-chains 82 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 0.2980 chunk 43 optimal weight: 0.0970 chunk 117 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 HIS A 421 HIS ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 HIS ** B 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12817 Z= 0.202 Angle : 0.693 11.203 17388 Z= 0.348 Chirality : 0.045 0.183 1922 Planarity : 0.005 0.064 2261 Dihedral : 6.220 75.344 1707 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 2.35 % Allowed : 13.68 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.22), residues: 1562 helix: 0.39 (0.19), residues: 714 sheet: -0.64 (0.28), residues: 340 loop : -1.22 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 231 HIS 0.005 0.001 HIS A 77 PHE 0.023 0.002 PHE B 602 TYR 0.011 0.001 TYR B 454 ARG 0.006 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: -0.1583 (ptm) cc_final: -0.1849 (ptt) REVERT: A 43 MET cc_start: 0.2830 (mpp) cc_final: 0.1728 (mmt) REVERT: A 95 MET cc_start: 0.6581 (tmm) cc_final: 0.5721 (tmm) REVERT: A 113 PHE cc_start: 0.5322 (t80) cc_final: 0.5072 (t80) REVERT: A 682 MET cc_start: 0.7622 (mmm) cc_final: 0.7319 (mmp) REVERT: A 698 MET cc_start: 0.8619 (mpp) cc_final: 0.8371 (mpp) REVERT: B 31 MET cc_start: 0.2123 (OUTLIER) cc_final: 0.1316 (mmp) REVERT: B 308 MET cc_start: 0.8000 (pmm) cc_final: 0.7796 (pmm) outliers start: 32 outliers final: 9 residues processed: 112 average time/residue: 0.2875 time to fit residues: 47.5597 Evaluate side-chains 89 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 693 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 67 optimal weight: 0.7980 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 HIS B 397 ASN B 653 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12817 Z= 0.226 Angle : 0.692 10.434 17388 Z= 0.345 Chirality : 0.044 0.191 1922 Planarity : 0.005 0.078 2261 Dihedral : 6.122 72.467 1707 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.19 % Favored : 94.69 % Rotamer: Outliers : 2.79 % Allowed : 13.53 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1562 helix: 0.51 (0.19), residues: 715 sheet: -0.54 (0.28), residues: 338 loop : -1.23 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 665 HIS 0.007 0.001 HIS B 152 PHE 0.023 0.002 PHE A 602 TYR 0.012 0.001 TYR B 454 ARG 0.005 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 79 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: -0.1816 (ptm) cc_final: -0.2058 (ptt) REVERT: A 43 MET cc_start: 0.2838 (mpp) cc_final: 0.1703 (mmt) REVERT: A 95 MET cc_start: 0.6573 (tmm) cc_final: 0.6053 (tmm) REVERT: A 113 PHE cc_start: 0.5516 (t80) cc_final: 0.5248 (t80) REVERT: A 209 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8725 (tp) REVERT: A 456 CYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6761 (t) REVERT: B 31 MET cc_start: 0.3476 (mmp) cc_final: 0.2507 (mmp) REVERT: B 43 MET cc_start: 0.1373 (mtp) cc_final: -0.0040 (mpp) REVERT: B 67 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8166 (ptt) REVERT: B 177 PHE cc_start: 0.8294 (m-10) cc_final: 0.8010 (m-10) REVERT: B 253 PHE cc_start: 0.7067 (m-80) cc_final: 0.6618 (m-10) REVERT: B 542 MET cc_start: 0.8521 (ptt) cc_final: 0.7398 (ptt) REVERT: B 545 MET cc_start: 0.8326 (tmm) cc_final: 0.7946 (ppp) outliers start: 38 outliers final: 19 residues processed: 111 average time/residue: 0.3247 time to fit residues: 52.8535 Evaluate side-chains 96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 205 ARG Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 2 optimal weight: 20.0000 chunk 112 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 76 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 657 GLN ** B 693 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12817 Z= 0.206 Angle : 0.688 9.231 17388 Z= 0.340 Chirality : 0.044 0.199 1922 Planarity : 0.005 0.069 2261 Dihedral : 6.027 71.698 1707 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 2.35 % Allowed : 14.41 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.22), residues: 1562 helix: 0.61 (0.19), residues: 711 sheet: -0.56 (0.27), residues: 344 loop : -1.14 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 110 HIS 0.008 0.001 HIS B 152 PHE 0.023 0.002 PHE A 602 TYR 0.009 0.001 TYR B 454 ARG 0.015 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 74 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.2819 (mpp) cc_final: 0.1674 (mmt) REVERT: A 113 PHE cc_start: 0.5492 (t80) cc_final: 0.5213 (t80) REVERT: A 209 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8725 (tp) REVERT: A 308 MET cc_start: 0.8644 (tpp) cc_final: 0.8356 (mmm) REVERT: B 31 MET cc_start: 0.4761 (mmp) cc_final: 0.4403 (mmp) REVERT: B 43 MET cc_start: 0.1380 (mtp) cc_final: -0.0103 (mpp) REVERT: B 53 TRP cc_start: 0.7568 (m-90) cc_final: 0.7285 (m-90) REVERT: B 67 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8118 (ptt) REVERT: B 177 PHE cc_start: 0.8266 (m-10) cc_final: 0.7973 (m-10) REVERT: B 221 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7975 (mt) REVERT: B 253 PHE cc_start: 0.7033 (m-80) cc_final: 0.6677 (m-10) REVERT: B 273 MET cc_start: 0.7515 (tpt) cc_final: 0.7216 (tpt) REVERT: B 545 MET cc_start: 0.8346 (tmm) cc_final: 0.8030 (ppp) outliers start: 32 outliers final: 19 residues processed: 102 average time/residue: 0.2446 time to fit residues: 38.2627 Evaluate side-chains 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 0.6980 chunk 135 optimal weight: 0.0030 chunk 29 optimal weight: 10.0000 chunk 88 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 150 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 10.0000 overall best weight: 0.5068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 12817 Z= 0.186 Angle : 0.702 9.314 17388 Z= 0.341 Chirality : 0.045 0.258 1922 Planarity : 0.005 0.062 2261 Dihedral : 5.954 72.083 1707 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.99 % Favored : 94.94 % Rotamer: Outliers : 2.13 % Allowed : 14.85 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1562 helix: 0.78 (0.20), residues: 701 sheet: -0.60 (0.27), residues: 341 loop : -1.03 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 231 HIS 0.005 0.001 HIS B 152 PHE 0.022 0.001 PHE A 602 TYR 0.006 0.001 TYR B 454 ARG 0.006 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.2807 (mpp) cc_final: 0.1655 (mmt) REVERT: A 113 PHE cc_start: 0.5430 (t80) cc_final: 0.5108 (t80) REVERT: A 209 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8716 (tp) REVERT: A 456 CYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6294 (t) REVERT: B 31 MET cc_start: 0.4341 (OUTLIER) cc_final: 0.4106 (mmp) REVERT: B 43 MET cc_start: 0.1440 (mtp) cc_final: -0.0053 (mpp) REVERT: B 53 TRP cc_start: 0.7538 (m-90) cc_final: 0.7273 (m-90) REVERT: B 253 PHE cc_start: 0.6640 (m-80) cc_final: 0.6117 (m-80) REVERT: B 273 MET cc_start: 0.7472 (tpt) cc_final: 0.7106 (tpt) REVERT: B 772 MET cc_start: 0.8493 (mtm) cc_final: 0.8227 (ptp) outliers start: 29 outliers final: 22 residues processed: 99 average time/residue: 0.2520 time to fit residues: 37.5693 Evaluate side-chains 97 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 31 MET Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 466 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 0.1980 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12817 Z= 0.182 Angle : 0.712 13.810 17388 Z= 0.342 Chirality : 0.044 0.205 1922 Planarity : 0.005 0.057 2261 Dihedral : 5.893 72.433 1707 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.06 % Allowed : 15.66 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1562 helix: 0.80 (0.20), residues: 716 sheet: -0.43 (0.28), residues: 335 loop : -1.08 (0.30), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 110 HIS 0.004 0.001 HIS B 152 PHE 0.023 0.001 PHE A 602 TYR 0.008 0.001 TYR B 415 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.2801 (mpp) cc_final: 0.1622 (mmt) REVERT: A 113 PHE cc_start: 0.5453 (t80) cc_final: 0.5121 (t80) REVERT: A 209 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8723 (tp) REVERT: A 456 CYS cc_start: 0.6826 (OUTLIER) cc_final: 0.6308 (t) REVERT: B 43 MET cc_start: 0.1437 (mtp) cc_final: -0.0068 (mpp) REVERT: B 53 TRP cc_start: 0.7610 (m-90) cc_final: 0.7367 (m-90) REVERT: B 273 MET cc_start: 0.7434 (tpt) cc_final: 0.7178 (tpt) outliers start: 28 outliers final: 20 residues processed: 98 average time/residue: 0.2395 time to fit residues: 36.2099 Evaluate side-chains 96 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 0.0770 chunk 45 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 95 optimal weight: 0.2980 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 0.0770 chunk 144 optimal weight: 0.6980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12817 Z= 0.174 Angle : 0.714 9.986 17388 Z= 0.345 Chirality : 0.044 0.181 1922 Planarity : 0.005 0.070 2261 Dihedral : 5.860 73.393 1707 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.91 % Allowed : 16.10 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1562 helix: 0.84 (0.20), residues: 715 sheet: -0.25 (0.28), residues: 331 loop : -1.11 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 110 HIS 0.005 0.001 HIS B 152 PHE 0.021 0.001 PHE B 602 TYR 0.006 0.001 TYR B 415 ARG 0.003 0.000 ARG A 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.2791 (mpp) cc_final: 0.2127 (mpp) REVERT: A 113 PHE cc_start: 0.5369 (t80) cc_final: 0.5020 (t80) REVERT: A 209 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8707 (tp) REVERT: A 251 MET cc_start: 0.6960 (tpt) cc_final: 0.6704 (tpt) REVERT: A 456 CYS cc_start: 0.6823 (OUTLIER) cc_final: 0.6204 (t) REVERT: B 53 TRP cc_start: 0.7602 (m-90) cc_final: 0.7370 (m-90) REVERT: B 273 MET cc_start: 0.7608 (OUTLIER) cc_final: 0.7400 (tpt) REVERT: B 545 MET cc_start: 0.8306 (tmm) cc_final: 0.7856 (ppp) outliers start: 26 outliers final: 19 residues processed: 94 average time/residue: 0.2319 time to fit residues: 34.1322 Evaluate side-chains 94 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 110 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 126 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12817 Z= 0.189 Angle : 0.712 10.543 17388 Z= 0.343 Chirality : 0.044 0.277 1922 Planarity : 0.005 0.048 2261 Dihedral : 5.816 73.862 1707 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.21 % Allowed : 16.03 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.22), residues: 1562 helix: 0.89 (0.20), residues: 714 sheet: -0.22 (0.28), residues: 333 loop : -1.10 (0.29), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 665 HIS 0.004 0.001 HIS B 152 PHE 0.025 0.001 PHE B 177 TYR 0.008 0.001 TYR B 415 ARG 0.004 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.2792 (mpp) cc_final: 0.2120 (mpp) REVERT: A 113 PHE cc_start: 0.5395 (t80) cc_final: 0.5099 (t80) REVERT: A 209 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8736 (tp) REVERT: A 456 CYS cc_start: 0.6899 (OUTLIER) cc_final: 0.6337 (t) REVERT: B 43 MET cc_start: 0.1236 (mtp) cc_final: 0.0809 (mpp) REVERT: B 53 TRP cc_start: 0.7652 (m-90) cc_final: 0.7410 (m-90) REVERT: B 273 MET cc_start: 0.7655 (OUTLIER) cc_final: 0.7422 (tpt) REVERT: B 419 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8317 (p) REVERT: B 545 MET cc_start: 0.8340 (tmm) cc_final: 0.7960 (ppp) outliers start: 30 outliers final: 19 residues processed: 100 average time/residue: 0.2434 time to fit residues: 36.9956 Evaluate side-chains 93 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 273 MET Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 70 optimal weight: 0.0270 chunk 102 optimal weight: 0.9990 chunk 155 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 overall best weight: 0.7442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12817 Z= 0.189 Angle : 0.757 10.899 17388 Z= 0.365 Chirality : 0.045 0.313 1922 Planarity : 0.005 0.089 2261 Dihedral : 5.875 74.331 1707 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.91 % Allowed : 16.25 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.22), residues: 1562 helix: 0.83 (0.20), residues: 716 sheet: -0.16 (0.28), residues: 333 loop : -1.11 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 665 HIS 0.005 0.001 HIS B 365 PHE 0.022 0.001 PHE A 602 TYR 0.008 0.001 TYR B 415 ARG 0.006 0.000 ARG B 358 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 MET cc_start: 0.2983 (mpp) cc_final: 0.2412 (mpp) REVERT: A 113 PHE cc_start: 0.5396 (t80) cc_final: 0.5066 (t80) REVERT: A 209 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8742 (tp) REVERT: A 251 MET cc_start: 0.6944 (tpt) cc_final: 0.5833 (tpt) REVERT: A 456 CYS cc_start: 0.6926 (OUTLIER) cc_final: 0.6393 (t) REVERT: B 43 MET cc_start: 0.1309 (mtp) cc_final: 0.0269 (mpp) REVERT: B 53 TRP cc_start: 0.7667 (m-90) cc_final: 0.7421 (m-90) REVERT: B 273 MET cc_start: 0.7617 (tpt) cc_final: 0.7399 (tpt) REVERT: B 419 VAL cc_start: 0.8667 (OUTLIER) cc_final: 0.8304 (p) REVERT: B 545 MET cc_start: 0.8335 (tmm) cc_final: 0.7969 (ppp) outliers start: 26 outliers final: 21 residues processed: 94 average time/residue: 0.2222 time to fit residues: 33.2543 Evaluate side-chains 95 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 71 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 GLN Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 306 ASN Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 456 CYS Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 615 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain B residue 142 GLN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 419 VAL Chi-restraints excluded: chain B residue 452 ASP Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 685 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN A 289 ASN ** A 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 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 = 0.3695 r_free = 0.3695 target = 0.066390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.043468 restraints weight = 98147.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.042847 restraints weight = 77970.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.043148 restraints weight = 61610.984| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 12817 Z= 0.306 Angle : 0.811 17.770 17388 Z= 0.396 Chirality : 0.046 0.267 1922 Planarity : 0.005 0.068 2261 Dihedral : 5.967 72.841 1707 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.91 % Allowed : 16.40 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.22), residues: 1562 helix: 0.71 (0.20), residues: 720 sheet: -0.33 (0.28), residues: 336 loop : -0.99 (0.30), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 665 HIS 0.005 0.001 HIS B 365 PHE 0.028 0.002 PHE A 602 TYR 0.013 0.001 TYR B 415 ARG 0.006 0.001 ARG A 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.02 seconds wall clock time: 42 minutes 45.77 seconds (2565.77 seconds total)