Starting phenix.real_space_refine on Wed Feb 4 16:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qhi_53170/02_2026/9qhi_53170_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qhi_53170/02_2026/9qhi_53170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9qhi_53170/02_2026/9qhi_53170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qhi_53170/02_2026/9qhi_53170.map" model { file = "/net/cci-nas-00/data/ceres_data/9qhi_53170/02_2026/9qhi_53170_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qhi_53170/02_2026/9qhi_53170_neut.cif" } resolution = 4.27 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= 0.001 sd= 0.015 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 P 7 5.49 5 S 52 5.16 5 C 7252 2.51 5 N 1933 2.21 5 O 2175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11419 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2330 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 274} Chain: "B" Number of atoms: 7826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 987, 7826 Classifications: {'peptide': 987} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 47, 'TRANS': 934} Chain breaks: 1 Chain: "C" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.39, per 1000 atoms: 0.21 Number of scatterers: 11419 At special positions: 0 Unit cell: (90.1, 100.3, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 7 15.00 O 2175 8.00 N 1933 7.00 C 7252 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 444.0 milliseconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 11 sheets defined 48.0% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 4523 through 4535 removed outlier: 3.813A pdb=" N LYS A4534 " --> pdb=" O ALA A4530 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A4535 " --> pdb=" O VAL A4531 " (cutoff:3.500A) Processing helix chain 'A' and resid 4559 through 4566 Processing helix chain 'A' and resid 4572 through 4588 removed outlier: 3.807A pdb=" N VAL A4583 " --> pdb=" O ALA A4579 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR A4584 " --> pdb=" O GLN A4580 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR A4587 " --> pdb=" O VAL A4583 " (cutoff:3.500A) Processing helix chain 'A' and resid 4676 through 4680 removed outlier: 3.554A pdb=" N LYS A4680 " --> pdb=" O PRO A4677 " (cutoff:3.500A) Processing helix chain 'A' and resid 4687 through 4700 removed outlier: 3.576A pdb=" N VAL A4695 " --> pdb=" O VAL A4691 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLN A4696 " --> pdb=" O LEU A4692 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER A4697 " --> pdb=" O VAL A4693 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A4698 " --> pdb=" O SER A4694 " (cutoff:3.500A) Processing helix chain 'A' and resid 4703 through 4708 removed outlier: 3.501A pdb=" N GLU A4708 " --> pdb=" O TYR A4705 " (cutoff:3.500A) Processing helix chain 'A' and resid 4711 through 4715 Processing helix chain 'A' and resid 4717 through 4739 Processing helix chain 'A' and resid 4740 through 4746 Processing helix chain 'A' and resid 4751 through 4779 removed outlier: 3.655A pdb=" N LEU A4761 " --> pdb=" O LYS A4757 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N VAL A4764 " --> pdb=" O TYR A4760 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLU A4765 " --> pdb=" O LEU A4761 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A4778 " --> pdb=" O ILE A4774 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A4779 " --> pdb=" O ALA A4775 " (cutoff:3.500A) Processing helix chain 'A' and resid 4786 through 4810 removed outlier: 3.555A pdb=" N GLN A4803 " --> pdb=" O ARG A4799 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A4806 " --> pdb=" O ALA A4802 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 52 removed outlier: 7.237A pdb=" N ARG B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLN B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 49 " --> pdb=" O SER B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 97 through 103 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.107A pdb=" N VAL B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.670A pdb=" N ALA B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B 128 " --> pdb=" O LYS B 124 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 301 through 307 removed outlier: 3.751A pdb=" N LYS B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 removed outlier: 3.677A pdb=" N GLU B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.540A pdb=" N THR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 387 through 408 removed outlier: 3.601A pdb=" N ALA B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 427 removed outlier: 3.820A pdb=" N SER B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 443 through 451 Processing helix chain 'B' and resid 451 through 459 Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.575A pdb=" N GLU B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.547A pdb=" N ILE B 517 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 533 Processing helix chain 'B' and resid 547 through 552 removed outlier: 4.144A pdb=" N THR B 551 " --> pdb=" O THR B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 583 removed outlier: 3.680A pdb=" N ARG B 574 " --> pdb=" O ASN B 570 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 614 Processing helix chain 'B' and resid 623 through 629 Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.591A pdb=" N THR B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 Processing helix chain 'B' and resid 751 through 769 Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 779 through 788 Processing helix chain 'B' and resid 821 through 834 Processing helix chain 'B' and resid 857 through 873 Processing helix chain 'B' and resid 879 through 889 removed outlier: 3.579A pdb=" N THR B 883 " --> pdb=" O ASP B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 914 removed outlier: 3.639A pdb=" N THR B 898 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 910 " --> pdb=" O ALA B 906 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 921 Processing helix chain 'B' and resid 967 through 979 Processing helix chain 'B' and resid 1001 through 1007 removed outlier: 3.592A pdb=" N LEU B1007 " --> pdb=" O ARG B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1014 Processing helix chain 'C' and resid 22 through 30 removed outlier: 3.590A pdb=" N VAL C 26 " --> pdb=" O THR C 22 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 28 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.158A pdb=" N GLU C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 35 removed outlier: 4.050A pdb=" N ILE E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.569A pdb=" N GLN E 41 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.520A pdb=" N TYR E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4540 removed outlier: 3.589A pdb=" N ASP A4538 " --> pdb=" O VAL A4599 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP A4602 " --> pdb=" O ILE A4608 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE A4608 " --> pdb=" O ASP A4602 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4543 through 4545 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 136 removed outlier: 6.161A pdb=" N VAL B 64 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N CYS B 156 " --> pdb=" O HIS B 63 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 186 " --> pdb=" O LEU B 159 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 202 through 205 Processing sheet with id=AA5, first strand: chain 'B' and resid 260 through 262 removed outlier: 3.555A pdb=" N LEU B 245 " --> pdb=" O GLN B 261 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 229 " --> pdb=" O PHE B 271 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N SER B 272 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 265 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.253A pdb=" N ILE B 493 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N HIS B 541 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL B 495 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR B 496 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL B 563 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ILE B 564 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N SER B 591 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N THR B 566 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 8.928A pdb=" N THR B 593 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N CYS B 924 " --> pdb=" O THR B 600 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 944 through 947 removed outlier: 6.601A pdb=" N ILE B 950 " --> pdb=" O ILE B 946 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.493A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 985 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL B 986 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.493A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 12 through 16 removed outlier: 3.592A pdb=" N LEU C 15 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 67 " --> pdb=" O PHE C 4 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG C 42 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 12 through 16 removed outlier: 3.839A pdb=" N LEU E 69 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG E 42 " --> pdb=" O VAL E 70 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.05 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3719 1.34 - 1.46: 2374 1.46 - 1.58: 5490 1.58 - 1.70: 7 1.70 - 1.82: 77 Bond restraints: 11667 Sorted by residual: bond pdb=" N GLY C 75 " pdb=" CA GLY C 75 " ideal model delta sigma weight residual 1.446 1.474 -0.028 1.06e-02 8.90e+03 7.04e+00 bond pdb=" CZ ARG C 74 " pdb=" NH2 ARG C 74 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.72e+00 bond pdb=" CA ILE B 622 " pdb=" C ILE B 622 " ideal model delta sigma weight residual 1.524 1.544 -0.020 9.30e-03 1.16e+04 4.56e+00 bond pdb=" CZ2 TRP A4673 " pdb=" CH2 TRP A4673 " ideal model delta sigma weight residual 1.368 1.404 -0.036 1.90e-02 2.77e+03 3.61e+00 bond pdb=" CG TRP A4673 " pdb=" CD2 TRP A4673 " ideal model delta sigma weight residual 1.433 1.467 -0.034 1.80e-02 3.09e+03 3.54e+00 ... (remaining 11662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 15569 2.07 - 4.14: 219 4.14 - 6.21: 22 6.21 - 8.28: 3 8.28 - 10.35: 2 Bond angle restraints: 15815 Sorted by residual: angle pdb=" CA ASN A4671 " pdb=" CB ASN A4671 " pdb=" CG ASN A4671 " ideal model delta sigma weight residual 112.60 117.65 -5.05 1.00e+00 1.00e+00 2.55e+01 angle pdb=" C PHE B 624 " pdb=" N SER B 625 " pdb=" CA SER B 625 " ideal model delta sigma weight residual 120.38 125.46 -5.08 1.37e+00 5.33e-01 1.38e+01 angle pdb=" CB MET B 844 " pdb=" CG MET B 844 " pdb=" SD MET B 844 " ideal model delta sigma weight residual 112.70 102.35 10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" N PRO B 623 " pdb=" CA PRO B 623 " pdb=" CB PRO B 623 " ideal model delta sigma weight residual 103.25 106.22 -2.97 8.80e-01 1.29e+00 1.14e+01 angle pdb=" C GLY C 75 " pdb=" N ALA C 76 " pdb=" CA ALA C 76 " ideal model delta sigma weight residual 121.70 127.73 -6.03 1.80e+00 3.09e-01 1.12e+01 ... (remaining 15810 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 6590 16.96 - 33.93: 423 33.93 - 50.89: 72 50.89 - 67.86: 17 67.86 - 84.82: 7 Dihedral angle restraints: 7109 sinusoidal: 2931 harmonic: 4178 Sorted by residual: dihedral pdb=" C4' AMP E 101 " pdb=" C5' AMP E 101 " pdb=" O5' AMP E 101 " pdb=" P AMP E 101 " ideal model delta sinusoidal sigma weight residual 180.00 109.52 70.48 1 2.00e+01 2.50e-03 1.60e+01 dihedral pdb=" CA ILE C 44 " pdb=" C ILE C 44 " pdb=" N PHE C 45 " pdb=" CA PHE C 45 " ideal model delta harmonic sigma weight residual 180.00 160.73 19.27 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA MET B 69 " pdb=" C MET B 69 " pdb=" N GLY B 70 " pdb=" CA GLY B 70 " ideal model delta harmonic sigma weight residual 180.00 163.67 16.33 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 7106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1457 0.051 - 0.102: 263 0.102 - 0.153: 53 0.153 - 0.204: 6 0.204 - 0.254: 2 Chirality restraints: 1781 Sorted by residual: chirality pdb=" CA ILE B 622 " pdb=" N ILE B 622 " pdb=" C ILE B 622 " pdb=" CB ILE B 622 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" C3' AMP E 101 " pdb=" C2' AMP E 101 " pdb=" C4' AMP E 101 " pdb=" O3' AMP E 101 " both_signs ideal model delta sigma weight residual False -2.51 -2.74 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA PRO B 623 " pdb=" N PRO B 623 " pdb=" C PRO B 623 " pdb=" CB PRO B 623 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.74e-01 ... (remaining 1778 not shown) Planarity restraints: 2028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A4673 " 0.081 2.00e-02 2.50e+03 4.08e-02 4.17e+01 pdb=" CG TRP A4673 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A4673 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP A4673 " -0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP A4673 " -0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP A4673 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A4673 " -0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4673 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4673 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A4673 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A4660 " -0.059 2.00e-02 2.50e+03 3.40e-02 2.31e+01 pdb=" CG TYR A4660 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A4660 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR A4660 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR A4660 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR A4660 " 0.026 2.00e-02 2.50e+03 pdb=" CZ TYR A4660 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A4660 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 625 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C SER B 625 " -0.030 2.00e-02 2.50e+03 pdb=" O SER B 625 " 0.011 2.00e-02 2.50e+03 pdb=" N THR B 626 " 0.010 2.00e-02 2.50e+03 ... (remaining 2025 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 4 2.04 - 2.76: 1638 2.76 - 3.47: 17387 3.47 - 4.19: 26896 4.19 - 4.90: 47296 Nonbonded interactions: 93221 Sorted by model distance: nonbonded pdb=" OG SER B 625 " pdb=" C ALA C 76 " model vdw 1.329 3.270 nonbonded pdb=" SG CYS A4666 " pdb=" CB ALA C 76 " model vdw 1.821 3.820 nonbonded pdb=" CH2 TRP A4673 " pdb=" N GLY A4675 " model vdw 1.956 3.420 nonbonded pdb=" CZ3 TRP A4673 " pdb=" N GLY A4675 " model vdw 1.992 3.420 nonbonded pdb=" CZ2 TRP A4673 " pdb=" CA GLY A4675 " model vdw 2.125 3.740 ... (remaining 93216 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 'C' selection = (chain 'E' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) } 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.560 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 0.048 11668 Z= 0.163 Angle : 0.590 10.355 15815 Z= 0.317 Chirality : 0.042 0.254 1781 Planarity : 0.004 0.041 2028 Dihedral : 12.025 84.822 4395 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.08 % Allowed : 0.63 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.24 (0.23), residues: 1420 helix: 1.74 (0.22), residues: 575 sheet: 0.10 (0.37), residues: 205 loop : 0.35 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 54 TYR 0.059 0.002 TYR A4660 PHE 0.018 0.002 PHE B 630 TRP 0.081 0.003 TRP A4673 HIS 0.016 0.001 HIS A4800 Details of bonding type rmsd covalent geometry : bond 0.00327 (11667) covalent geometry : angle 0.58986 (15815) hydrogen bonds : bond 0.17533 ( 515) hydrogen bonds : angle 6.65327 ( 1407) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9147 (mpp) cc_final: 0.8853 (mpp) REVERT: A 4627 GLU cc_start: 0.8835 (tt0) cc_final: 0.8419 (tp30) REVERT: A 4790 MET cc_start: 0.9625 (mmt) cc_final: 0.9109 (tpp) REVERT: B 69 MET cc_start: 0.9136 (mpp) cc_final: 0.8549 (mpp) REVERT: B 256 LEU cc_start: 0.8744 (tp) cc_final: 0.8348 (tp) REVERT: B 329 MET cc_start: 0.9059 (tpt) cc_final: 0.8798 (tpp) REVERT: B 475 MET cc_start: 0.9633 (mmp) cc_final: 0.9364 (mmm) REVERT: B 594 MET cc_start: 0.9473 (tmm) cc_final: 0.8595 (tmm) REVERT: B 616 ASP cc_start: 0.9659 (p0) cc_final: 0.9442 (t0) REVERT: B 872 MET cc_start: 0.9155 (mmp) cc_final: 0.8919 (tpp) REVERT: B 985 MET cc_start: 0.8805 (tmm) cc_final: 0.8571 (tmm) REVERT: B 1009 MET cc_start: 0.9384 (mmp) cc_final: 0.9169 (mmm) REVERT: C 1 MET cc_start: 0.7754 (ptm) cc_final: 0.7387 (ptm) REVERT: E 1 MET cc_start: 0.8692 (ttt) cc_final: 0.7791 (tpp) REVERT: E 6 LYS cc_start: 0.9740 (mtpp) cc_final: 0.9474 (mmtm) outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.1114 time to fit residues: 12.0520 Evaluate side-chains 59 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4769 GLN B 171 ASN B 234 ASN ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.030426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2540 r_free = 0.2540 target = 0.023593 restraints weight = 135819.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2561 r_free = 0.2561 target = 0.024119 restraints weight = 100353.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.024596 restraints weight = 80843.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.024967 restraints weight = 68363.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.025178 restraints weight = 59440.885| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.0925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11668 Z= 0.152 Angle : 0.545 6.595 15815 Z= 0.285 Chirality : 0.040 0.153 1781 Planarity : 0.004 0.035 2028 Dihedral : 5.124 64.405 1575 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.29 (0.23), residues: 1420 helix: 1.80 (0.22), residues: 589 sheet: 0.12 (0.37), residues: 201 loop : 0.33 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A4600 TYR 0.011 0.001 TYR B 611 PHE 0.020 0.001 PHE A4688 TRP 0.027 0.001 TRP A4673 HIS 0.006 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00315 (11667) covalent geometry : angle 0.54542 (15815) hydrogen bonds : bond 0.03730 ( 515) hydrogen bonds : angle 5.19013 ( 1407) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9262 (mpp) cc_final: 0.8899 (mpp) REVERT: A 4627 GLU cc_start: 0.8755 (tt0) cc_final: 0.8522 (tp30) REVERT: A 4790 MET cc_start: 0.9584 (mmt) cc_final: 0.9087 (tpp) REVERT: B 69 MET cc_start: 0.9161 (mpp) cc_final: 0.8549 (mpp) REVERT: B 256 LEU cc_start: 0.8746 (tp) cc_final: 0.8357 (tp) REVERT: B 329 MET cc_start: 0.9043 (tpt) cc_final: 0.8770 (tpp) REVERT: B 401 GLU cc_start: 0.9499 (mm-30) cc_final: 0.9295 (mm-30) REVERT: B 475 MET cc_start: 0.9642 (mmp) cc_final: 0.9374 (mmm) REVERT: B 594 MET cc_start: 0.9419 (tmm) cc_final: 0.8524 (tmm) REVERT: B 985 MET cc_start: 0.8821 (tmm) cc_final: 0.8620 (tmm) REVERT: E 1 MET cc_start: 0.8636 (ttt) cc_final: 0.7712 (tpp) REVERT: E 6 LYS cc_start: 0.9754 (mtpp) cc_final: 0.9490 (mmtm) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1047 time to fit residues: 10.8588 Evaluate side-chains 57 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 49 optimal weight: 0.1980 chunk 93 optimal weight: 0.0470 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 117 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 128 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 overall best weight: 4.0484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4769 GLN B 171 ASN B 234 ASN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.030683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.023812 restraints weight = 139589.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.024400 restraints weight = 102207.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.024873 restraints weight = 80896.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.025187 restraints weight = 67936.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2587 r_free = 0.2587 target = 0.025450 restraints weight = 59580.849| |-----------------------------------------------------------------------------| r_work (final): 0.2573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11668 Z= 0.191 Angle : 0.580 7.827 15815 Z= 0.301 Chirality : 0.041 0.193 1781 Planarity : 0.004 0.045 2028 Dihedral : 5.213 72.362 1575 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.22 (0.23), residues: 1420 helix: 1.71 (0.22), residues: 589 sheet: 0.12 (0.37), residues: 195 loop : 0.30 (0.26), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 54 TYR 0.017 0.002 TYR A4621 PHE 0.014 0.002 PHE A4598 TRP 0.014 0.001 TRP A4673 HIS 0.004 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00393 (11667) covalent geometry : angle 0.58040 (15815) hydrogen bonds : bond 0.03579 ( 515) hydrogen bonds : angle 5.15775 ( 1407) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9245 (mpp) cc_final: 0.8903 (mpp) REVERT: A 4627 GLU cc_start: 0.8737 (tt0) cc_final: 0.8452 (tp30) REVERT: A 4790 MET cc_start: 0.9612 (mmt) cc_final: 0.9111 (tpp) REVERT: B 69 MET cc_start: 0.9195 (mpp) cc_final: 0.8391 (mpp) REVERT: B 253 MET cc_start: 0.9213 (mtp) cc_final: 0.8633 (mtt) REVERT: B 329 MET cc_start: 0.9056 (tpt) cc_final: 0.8766 (tpp) REVERT: B 475 MET cc_start: 0.9653 (mmp) cc_final: 0.9393 (mmm) REVERT: B 594 MET cc_start: 0.9417 (tmm) cc_final: 0.9157 (tmm) REVERT: E 1 MET cc_start: 0.8595 (ttt) cc_final: 0.7677 (tpp) REVERT: E 6 LYS cc_start: 0.9759 (mtpp) cc_final: 0.9477 (mmtm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1001 time to fit residues: 10.4476 Evaluate side-chains 53 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 12 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 138 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 109 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4558 HIS A4769 GLN B 171 ASN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.030223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2516 r_free = 0.2516 target = 0.023332 restraints weight = 139138.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2541 r_free = 0.2541 target = 0.023942 restraints weight = 102520.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2557 r_free = 0.2557 target = 0.024369 restraints weight = 81447.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.024715 restraints weight = 68491.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.024895 restraints weight = 59633.041| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11668 Z= 0.175 Angle : 0.559 6.818 15815 Z= 0.290 Chirality : 0.040 0.162 1781 Planarity : 0.004 0.046 2028 Dihedral : 5.208 76.129 1575 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.17 (0.23), residues: 1420 helix: 1.65 (0.22), residues: 589 sheet: -0.03 (0.36), residues: 206 loop : 0.36 (0.27), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.013 0.002 TYR A4559 PHE 0.025 0.002 PHE A4688 TRP 0.013 0.001 TRP B 660 HIS 0.004 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00360 (11667) covalent geometry : angle 0.55878 (15815) hydrogen bonds : bond 0.03207 ( 515) hydrogen bonds : angle 4.99182 ( 1407) Misc. bond : bond 0.00016 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9168 (mpp) cc_final: 0.8766 (mpp) REVERT: A 4627 GLU cc_start: 0.8626 (tt0) cc_final: 0.8405 (tp30) REVERT: A 4790 MET cc_start: 0.9629 (mmt) cc_final: 0.9258 (mmp) REVERT: B 69 MET cc_start: 0.9139 (mpp) cc_final: 0.8734 (mpp) REVERT: B 253 MET cc_start: 0.9190 (mtp) cc_final: 0.8654 (mtt) REVERT: B 256 LEU cc_start: 0.8751 (tp) cc_final: 0.8541 (tp) REVERT: B 329 MET cc_start: 0.9028 (tpt) cc_final: 0.8730 (tpp) REVERT: B 475 MET cc_start: 0.9627 (mmp) cc_final: 0.9395 (mmm) REVERT: B 594 MET cc_start: 0.9426 (tmm) cc_final: 0.9080 (tmm) REVERT: B 616 ASP cc_start: 0.9507 (p0) cc_final: 0.9178 (t0) REVERT: E 1 MET cc_start: 0.8667 (ttt) cc_final: 0.7744 (tpp) REVERT: E 6 LYS cc_start: 0.9763 (mtpp) cc_final: 0.9487 (mmtm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0952 time to fit residues: 9.6608 Evaluate side-chains 52 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 43 optimal weight: 5.9990 chunk 124 optimal weight: 0.0980 chunk 109 optimal weight: 9.9990 chunk 18 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 97 optimal weight: 0.0060 chunk 51 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4769 GLN B 171 ASN ** C 68 HIS ** 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 = 0.2782 r_free = 0.2782 target = 0.031498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.024514 restraints weight = 137218.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.025132 restraints weight = 99941.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.025592 restraints weight = 79235.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2592 r_free = 0.2592 target = 0.025863 restraints weight = 66296.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.026155 restraints weight = 58592.362| |-----------------------------------------------------------------------------| r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11668 Z= 0.106 Angle : 0.501 6.285 15815 Z= 0.255 Chirality : 0.040 0.157 1781 Planarity : 0.003 0.046 2028 Dihedral : 4.965 75.237 1575 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.46 (0.24), residues: 1420 helix: 1.98 (0.22), residues: 584 sheet: 0.22 (0.37), residues: 195 loop : 0.37 (0.27), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 48 TYR 0.014 0.001 TYR A4621 PHE 0.015 0.001 PHE B 881 TRP 0.012 0.001 TRP A4673 HIS 0.003 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00226 (11667) covalent geometry : angle 0.50108 (15815) hydrogen bonds : bond 0.02869 ( 515) hydrogen bonds : angle 4.70555 ( 1407) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9354 (mpp) cc_final: 0.9005 (mpp) REVERT: A 4627 GLU cc_start: 0.8624 (tt0) cc_final: 0.8376 (tp30) REVERT: A 4790 MET cc_start: 0.9643 (mmt) cc_final: 0.9301 (mmp) REVERT: B 69 MET cc_start: 0.9157 (mpp) cc_final: 0.8719 (mpp) REVERT: B 253 MET cc_start: 0.9253 (mtp) cc_final: 0.8664 (mtt) REVERT: B 256 LEU cc_start: 0.8700 (tp) cc_final: 0.8461 (tp) REVERT: B 329 MET cc_start: 0.9047 (tpt) cc_final: 0.8771 (tpp) REVERT: B 475 MET cc_start: 0.9646 (mmp) cc_final: 0.9423 (mmm) REVERT: B 594 MET cc_start: 0.9435 (tmm) cc_final: 0.9115 (tmm) REVERT: E 1 MET cc_start: 0.8716 (ttt) cc_final: 0.7786 (tpp) REVERT: E 6 LYS cc_start: 0.9762 (mtpp) cc_final: 0.9468 (mmtp) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.0912 time to fit residues: 10.1548 Evaluate side-chains 55 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 51 optimal weight: 9.9990 chunk 136 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 10 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 59 optimal weight: 0.3980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4769 GLN B 171 ASN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 606 HIS ** C 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2762 r_free = 0.2762 target = 0.030225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.023445 restraints weight = 139330.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.024053 restraints weight = 100791.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2562 r_free = 0.2562 target = 0.024526 restraints weight = 79341.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.024853 restraints weight = 66209.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.025052 restraints weight = 57921.204| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11668 Z= 0.140 Angle : 0.524 7.189 15815 Z= 0.269 Chirality : 0.040 0.164 1781 Planarity : 0.003 0.046 2028 Dihedral : 4.962 76.848 1575 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.45 (0.24), residues: 1420 helix: 2.01 (0.22), residues: 584 sheet: 0.10 (0.36), residues: 206 loop : 0.39 (0.27), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 615 TYR 0.014 0.001 TYR A4621 PHE 0.013 0.001 PHE A4598 TRP 0.010 0.001 TRP A4673 HIS 0.004 0.001 HIS C 68 Details of bonding type rmsd covalent geometry : bond 0.00294 (11667) covalent geometry : angle 0.52398 (15815) hydrogen bonds : bond 0.02869 ( 515) hydrogen bonds : angle 4.72897 ( 1407) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9320 (mpp) cc_final: 0.8847 (mpp) REVERT: A 4627 GLU cc_start: 0.8634 (tt0) cc_final: 0.8413 (tp30) REVERT: A 4790 MET cc_start: 0.9618 (mmt) cc_final: 0.9259 (mmp) REVERT: B 69 MET cc_start: 0.9125 (mpp) cc_final: 0.8694 (mpp) REVERT: B 253 MET cc_start: 0.9218 (mtp) cc_final: 0.8647 (mtt) REVERT: B 256 LEU cc_start: 0.8781 (tp) cc_final: 0.8546 (tp) REVERT: B 329 MET cc_start: 0.9040 (tpt) cc_final: 0.8748 (tpp) REVERT: B 475 MET cc_start: 0.9629 (mmp) cc_final: 0.9423 (mmm) REVERT: B 594 MET cc_start: 0.9447 (tmm) cc_final: 0.9068 (tmm) REVERT: B 616 ASP cc_start: 0.9445 (p0) cc_final: 0.9170 (t0) REVERT: E 1 MET cc_start: 0.8637 (ttt) cc_final: 0.7883 (tpp) REVERT: E 6 LYS cc_start: 0.9755 (mtpp) cc_final: 0.9464 (mmtm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0934 time to fit residues: 9.3397 Evaluate side-chains 53 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 3 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 69 optimal weight: 6.9990 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4769 GLN B 171 ASN ** B 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 HIS ** 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 = 0.2766 r_free = 0.2766 target = 0.030586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.023741 restraints weight = 137905.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.024356 restraints weight = 100128.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.024810 restraints weight = 79169.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.025107 restraints weight = 66016.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.025398 restraints weight = 58269.714| |-----------------------------------------------------------------------------| r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11668 Z= 0.137 Angle : 0.528 7.820 15815 Z= 0.269 Chirality : 0.040 0.175 1781 Planarity : 0.003 0.045 2028 Dihedral : 4.953 77.993 1575 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.41 (0.24), residues: 1420 helix: 1.98 (0.22), residues: 584 sheet: -0.09 (0.37), residues: 205 loop : 0.42 (0.27), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 304 TYR 0.012 0.001 TYR A4621 PHE 0.013 0.001 PHE B 881 TRP 0.010 0.001 TRP A4673 HIS 0.009 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00285 (11667) covalent geometry : angle 0.52832 (15815) hydrogen bonds : bond 0.02818 ( 515) hydrogen bonds : angle 4.70445 ( 1407) Misc. bond : bond 0.00008 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9342 (mpp) cc_final: 0.8902 (mpp) REVERT: A 4627 GLU cc_start: 0.8640 (tt0) cc_final: 0.8401 (tp30) REVERT: A 4790 MET cc_start: 0.9630 (mmt) cc_final: 0.9264 (mmp) REVERT: B 329 MET cc_start: 0.9042 (tpt) cc_final: 0.8747 (tpp) REVERT: B 475 MET cc_start: 0.9623 (mmp) cc_final: 0.9411 (mmm) REVERT: B 594 MET cc_start: 0.9452 (tmm) cc_final: 0.9052 (tmm) REVERT: B 616 ASP cc_start: 0.9484 (p0) cc_final: 0.9176 (t0) REVERT: C 8 LEU cc_start: 0.9371 (pp) cc_final: 0.9072 (mm) REVERT: E 1 MET cc_start: 0.8649 (ttt) cc_final: 0.7876 (tpp) REVERT: E 6 LYS cc_start: 0.9755 (mtpp) cc_final: 0.9488 (mmtm) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0912 time to fit residues: 9.4969 Evaluate side-chains 55 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 125 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4769 GLN B 171 ASN ** C 68 HIS ** 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 = 0.2761 r_free = 0.2761 target = 0.030251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.023493 restraints weight = 136355.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.024104 restraints weight = 99033.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.024569 restraints weight = 78196.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.024927 restraints weight = 65259.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.025123 restraints weight = 56595.317| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11668 Z= 0.113 Angle : 0.516 8.570 15815 Z= 0.260 Chirality : 0.040 0.144 1781 Planarity : 0.003 0.045 2028 Dihedral : 4.873 77.632 1575 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.45 (0.24), residues: 1420 helix: 2.03 (0.22), residues: 583 sheet: -0.08 (0.37), residues: 205 loop : 0.43 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 304 TYR 0.012 0.001 TYR A4621 PHE 0.017 0.001 PHE B 645 TRP 0.011 0.001 TRP A4673 HIS 0.005 0.001 HIS B 308 Details of bonding type rmsd covalent geometry : bond 0.00240 (11667) covalent geometry : angle 0.51583 (15815) hydrogen bonds : bond 0.02742 ( 515) hydrogen bonds : angle 4.63553 ( 1407) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9324 (mpp) cc_final: 0.8852 (mpp) REVERT: A 4790 MET cc_start: 0.9632 (mmt) cc_final: 0.9240 (mmp) REVERT: B 329 MET cc_start: 0.9035 (tpt) cc_final: 0.8748 (tpp) REVERT: B 594 MET cc_start: 0.9447 (tmm) cc_final: 0.9082 (tmm) REVERT: B 616 ASP cc_start: 0.9506 (p0) cc_final: 0.9180 (t0) REVERT: E 1 MET cc_start: 0.8649 (ttt) cc_final: 0.7874 (tpp) REVERT: E 6 LYS cc_start: 0.9750 (mtpp) cc_final: 0.9481 (mmtm) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0991 time to fit residues: 10.3273 Evaluate side-chains 57 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 106 optimal weight: 0.0170 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 45 optimal weight: 0.0980 chunk 41 optimal weight: 0.0670 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4769 GLN B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.030737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2548 r_free = 0.2548 target = 0.024113 restraints weight = 135846.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.024772 restraints weight = 97037.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.025259 restraints weight = 75574.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.025621 restraints weight = 62308.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.025841 restraints weight = 53779.186| |-----------------------------------------------------------------------------| r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11668 Z= 0.088 Angle : 0.536 7.545 15815 Z= 0.264 Chirality : 0.040 0.143 1781 Planarity : 0.003 0.044 2028 Dihedral : 4.671 73.905 1575 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.47 (0.24), residues: 1420 helix: 2.02 (0.22), residues: 583 sheet: 0.08 (0.37), residues: 204 loop : 0.41 (0.27), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG A4605 TYR 0.013 0.001 TYR A4621 PHE 0.014 0.001 PHE B 656 TRP 0.015 0.001 TRP A4673 HIS 0.005 0.001 HIS B 858 Details of bonding type rmsd covalent geometry : bond 0.00181 (11667) covalent geometry : angle 0.53574 (15815) hydrogen bonds : bond 0.02624 ( 515) hydrogen bonds : angle 4.48349 ( 1407) Misc. bond : bond 0.00004 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9290 (mpp) cc_final: 0.8809 (mpp) REVERT: A 4560 MET cc_start: 0.8959 (mtm) cc_final: 0.8613 (mtt) REVERT: A 4790 MET cc_start: 0.9612 (mmt) cc_final: 0.9236 (mmp) REVERT: B 329 MET cc_start: 0.9009 (tpt) cc_final: 0.8753 (tpp) REVERT: B 475 MET cc_start: 0.9630 (mmp) cc_final: 0.9290 (mmm) REVERT: B 594 MET cc_start: 0.9402 (tmm) cc_final: 0.9115 (tmm) REVERT: B 616 ASP cc_start: 0.9498 (p0) cc_final: 0.9154 (t0) REVERT: C 8 LEU cc_start: 0.9388 (pp) cc_final: 0.9063 (mm) REVERT: E 1 MET cc_start: 0.8620 (ttt) cc_final: 0.7584 (tpp) REVERT: E 6 LYS cc_start: 0.9758 (mtpp) cc_final: 0.9500 (mmtm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0997 time to fit residues: 11.1501 Evaluate side-chains 58 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 121 optimal weight: 0.2980 chunk 29 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 0.0060 chunk 129 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4769 GLN B 171 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.031284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2558 r_free = 0.2558 target = 0.024611 restraints weight = 136916.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.025265 restraints weight = 97574.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2600 r_free = 0.2600 target = 0.025688 restraints weight = 75865.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.026132 restraints weight = 62576.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2627 r_free = 0.2627 target = 0.026389 restraints weight = 53872.499| |-----------------------------------------------------------------------------| r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11668 Z= 0.084 Angle : 0.519 7.519 15815 Z= 0.255 Chirality : 0.040 0.141 1781 Planarity : 0.003 0.047 2028 Dihedral : 4.521 70.453 1575 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.50 (0.24), residues: 1420 helix: 2.01 (0.22), residues: 585 sheet: 0.17 (0.38), residues: 200 loop : 0.43 (0.27), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A4605 TYR 0.015 0.001 TYR B 154 PHE 0.016 0.001 PHE B 656 TRP 0.014 0.001 TRP A4673 HIS 0.004 0.001 HIS B 858 Details of bonding type rmsd covalent geometry : bond 0.00180 (11667) covalent geometry : angle 0.51943 (15815) hydrogen bonds : bond 0.02598 ( 515) hydrogen bonds : angle 4.38883 ( 1407) Misc. bond : bond 0.00008 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4542 MET cc_start: 0.9278 (mpp) cc_final: 0.8736 (mpp) REVERT: A 4560 MET cc_start: 0.8962 (mtm) cc_final: 0.8627 (mtt) REVERT: A 4790 MET cc_start: 0.9610 (mmt) cc_final: 0.9228 (mmp) REVERT: B 253 MET cc_start: 0.9099 (mpp) cc_final: 0.8643 (mpp) REVERT: B 329 MET cc_start: 0.8980 (tpt) cc_final: 0.8720 (tpp) REVERT: B 475 MET cc_start: 0.9616 (mmp) cc_final: 0.9223 (mmm) REVERT: B 594 MET cc_start: 0.9394 (tmm) cc_final: 0.9118 (tmm) REVERT: B 616 ASP cc_start: 0.9480 (p0) cc_final: 0.9138 (t0) REVERT: C 8 LEU cc_start: 0.9383 (pp) cc_final: 0.9059 (mm) REVERT: C 67 LEU cc_start: 0.9074 (pt) cc_final: 0.8828 (pt) REVERT: E 1 MET cc_start: 0.8545 (ttt) cc_final: 0.7523 (tpp) REVERT: E 6 LYS cc_start: 0.9760 (mtpp) cc_final: 0.9507 (mmtm) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0965 time to fit residues: 10.4205 Evaluate side-chains 61 residues out of total 1265 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 47 optimal weight: 8.9990 chunk 113 optimal weight: 0.9990 chunk 112 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 121 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A4769 GLN B 171 ASN ** B 415 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 = 0.2776 r_free = 0.2776 target = 0.030704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2542 r_free = 0.2542 target = 0.024183 restraints weight = 139694.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.024817 restraints weight = 100105.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.025229 restraints weight = 78106.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.025658 restraints weight = 64698.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.025925 restraints weight = 55725.020| |-----------------------------------------------------------------------------| r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11668 Z= 0.101 Angle : 0.515 7.544 15815 Z= 0.256 Chirality : 0.039 0.140 1781 Planarity : 0.003 0.044 2028 Dihedral : 4.548 71.256 1575 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 0.07 % 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 are not related in a simple way. whole: 1.54 (0.24), residues: 1420 helix: 2.04 (0.23), residues: 592 sheet: -0.01 (0.37), residues: 208 loop : 0.53 (0.27), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A4605 TYR 0.016 0.001 TYR B 154 PHE 0.015 0.001 PHE A4598 TRP 0.009 0.001 TRP A4673 HIS 0.003 0.001 HIS B 858 Details of bonding type rmsd covalent geometry : bond 0.00219 (11667) covalent geometry : angle 0.51497 (15815) hydrogen bonds : bond 0.02605 ( 515) hydrogen bonds : angle 4.38486 ( 1407) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1662.59 seconds wall clock time: 29 minutes 50.58 seconds (1790.58 seconds total)