Starting phenix.real_space_refine on Tue Aug 4 23:03:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rw9_54304/08_2026/9rw9_54304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rw9_54304/08_2026/9rw9_54304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rw9_54304/08_2026/9rw9_54304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rw9_54304/08_2026/9rw9_54304.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rw9_54304/08_2026/9rw9_54304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rw9_54304/08_2026/9rw9_54304.map" } resolution = 4.2 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians P 98 5.49 5 C 3982 2.51 5 N 1378 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7192 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 265 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "B" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 265 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 222 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 10, 'TYR:plan': 1, 'GLN:plan1': 6, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 2277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 2277 Classifications: {'peptide': 460} Incomplete info: {'truncation_to_alanine': 407} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 448} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1499 Unresolved non-hydrogen angles: 1898 Unresolved non-hydrogen dihedrals: 1241 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLU:plan': 31, 'TYR:plan': 20, 'ARG:plan': 23, 'ASN:plan1': 21, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 10, 'GLN:plan1': 31, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 820 Chain: "D" Number of atoms: 2287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 2287 Classifications: {'peptide': 462} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 450} Chain breaks: 3 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1501 Unresolved non-hydrogen angles: 1899 Unresolved non-hydrogen dihedrals: 1242 Unresolved non-hydrogen chiralities: 130 Planarities with less than four sites: {'GLU:plan': 32, 'TYR:plan': 20, 'ARG:plan': 23, 'ASN:plan1': 21, 'PHE:plan': 18, 'ASP:plan': 26, 'HIS:plan': 9, 'GLN:plan1': 31, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 819 Chain: "E" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1049 Classifications: {'RNA': 50} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21} Link IDs: {'rna2p': 8, 'rna3p': 41} Chain breaks: 1 Chain: "F" Number of atoms: 1049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1049 Classifications: {'RNA': 50} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 7, 'rna3p_pur': 21, 'rna3p_pyr': 21} Link IDs: {'rna2p': 8, 'rna3p': 41} Chain breaks: 1 Time building chain proxies: 1.72, per 1000 atoms: 0.24 Number of scatterers: 7192 At special positions: 0 Unit cell: (88.956, 95.31, 169.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) P 98 15.00 O 1734 8.00 N 1378 7.00 C 3982 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.64 Conformation dependent library (CDL) restraints added in 445.9 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 69.6% alpha, 6.7% beta 40 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 695 through 746 Processing helix chain 'B' and resid 696 through 747 Processing helix chain 'C' and resid 6 through 25 removed outlier: 3.940A pdb=" N LYS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 37 Processing helix chain 'C' and resid 43 through 51 Processing helix chain 'C' and resid 53 through 63 Processing helix chain 'C' and resid 95 through 112 removed outlier: 3.786A pdb=" N TYR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 126 removed outlier: 3.847A pdb=" N LEU C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N HIS C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 138 removed outlier: 3.595A pdb=" N GLY C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 526 through 530 removed outlier: 3.501A pdb=" N THR C 530 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 554 Processing helix chain 'C' and resid 590 through 593 Processing helix chain 'C' and resid 594 through 599 removed outlier: 3.625A pdb=" N THR C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 608 removed outlier: 3.682A pdb=" N VAL C 605 " --> pdb=" O GLY C 601 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU C 606 " --> pdb=" O LEU C 602 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 607 " --> pdb=" O LYS C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 622 No H-bonds generated for 'chain 'C' and resid 620 through 622' Processing helix chain 'C' and resid 623 through 630 removed outlier: 3.651A pdb=" N LEU C 627 " --> pdb=" O ALA C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 652 Processing helix chain 'C' and resid 662 through 670 removed outlier: 3.545A pdb=" N CYS C 667 " --> pdb=" O LEU C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 680 removed outlier: 3.550A pdb=" N GLN C 680 " --> pdb=" O ILE C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 681 through 686 Processing helix chain 'C' and resid 690 through 694 Processing helix chain 'C' and resid 698 through 713 removed outlier: 4.038A pdb=" N TYR C 704 " --> pdb=" O GLU C 700 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY C 707 " --> pdb=" O LEU C 703 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 717 through 725 Processing helix chain 'C' and resid 726 through 728 No H-bonds generated for 'chain 'C' and resid 726 through 728' Processing helix chain 'C' and resid 729 through 746 removed outlier: 5.041A pdb=" N GLN C 744 " --> pdb=" O GLN C 740 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE C 745 " --> pdb=" O ILE C 741 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 773 removed outlier: 3.524A pdb=" N THR C 761 " --> pdb=" O ARG C 757 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR C 773 " --> pdb=" O LYS C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 782 through 789 removed outlier: 3.826A pdb=" N LEU C 787 " --> pdb=" O ILE C 784 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C 788 " --> pdb=" O ARG C 785 " (cutoff:3.500A) Processing helix chain 'C' and resid 793 through 802 removed outlier: 3.842A pdb=" N GLU C 798 " --> pdb=" O GLU C 794 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ARG C 799 " --> pdb=" O ASP C 795 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 800 " --> pdb=" O GLU C 796 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY C 802 " --> pdb=" O GLU C 798 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 816 removed outlier: 4.115A pdb=" N ALA C 807 " --> pdb=" O TYR C 803 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS C 808 " --> pdb=" O TYR C 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 25 Processing helix chain 'D' and resid 30 through 36 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 95 through 112 removed outlier: 3.611A pdb=" N GLU D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS D 107 " --> pdb=" O TYR D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 123 removed outlier: 3.670A pdb=" N LEU D 123 " --> pdb=" O VAL D 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 119 through 123' Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.610A pdb=" N GLN D 128 " --> pdb=" O HIS D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 138 Processing helix chain 'D' and resid 140 through 152 Processing helix chain 'D' and resid 521 through 529 removed outlier: 3.511A pdb=" N GLN D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 594 through 600 removed outlier: 4.411A pdb=" N THR D 598 " --> pdb=" O PRO D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 608 Processing helix chain 'D' and resid 618 through 630 removed outlier: 3.560A pdb=" N ASN D 624 " --> pdb=" O ASN D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 652 Processing helix chain 'D' and resid 654 through 658 Processing helix chain 'D' and resid 662 through 670 Processing helix chain 'D' and resid 677 through 688 removed outlier: 4.036A pdb=" N LEU D 681 " --> pdb=" O ILE D 677 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN D 683 " --> pdb=" O ASP D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 694 Processing helix chain 'D' and resid 698 through 714 removed outlier: 3.776A pdb=" N ASP D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 Processing helix chain 'D' and resid 726 through 743 removed outlier: 3.679A pdb=" N ARG D 730 " --> pdb=" O LYS D 726 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA D 731 " --> pdb=" O PRO D 727 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU D 732 " --> pdb=" O GLU D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 773 removed outlier: 3.809A pdb=" N SER D 764 " --> pdb=" O SER D 760 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR D 773 " --> pdb=" O LYS D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 787 removed outlier: 3.757A pdb=" N LEU D 787 " --> pdb=" O GLU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 790 No H-bonds generated for 'chain 'D' and resid 788 through 790' Processing helix chain 'D' and resid 793 through 801 Processing helix chain 'D' and resid 803 through 816 removed outlier: 3.714A pdb=" N LYS D 809 " --> pdb=" O LYS D 805 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'C' and resid 117 through 118 removed outlier: 3.882A pdb=" N VAL C 117 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 532 through 533 removed outlier: 3.922A pdb=" N GLU C 584 " --> pdb=" O THR C 580 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU C 572 " --> pdb=" O ILE C 565 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLU C 563 " --> pdb=" O THR C 574 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N ILE C 576 " --> pdb=" O ASP C 561 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP C 561 " --> pdb=" O ILE C 576 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE C 578 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER C 559 " --> pdb=" O ILE C 578 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LYS C 613 " --> pdb=" O PHE C 637 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 28 through 29 removed outlier: 3.575A pdb=" N ARG D 28 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 117 through 118 Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 533 removed outlier: 6.540A pdb=" N LYS D 613 " --> pdb=" O PHE D 637 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1395 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 1.19 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.29: 1139 1.29 - 1.37: 1516 1.37 - 1.45: 879 1.45 - 1.53: 3501 1.53 - 1.61: 387 Bond restraints: 7422 Sorted by residual: bond pdb=" C8 G E 50 " pdb=" N7 G E 50 " ideal model delta sigma weight residual 1.305 1.318 -0.013 6.00e-03 2.78e+04 4.39e+00 bond pdb=" C8 G E 18 " pdb=" N7 G E 18 " ideal model delta sigma weight residual 1.305 1.294 0.011 6.00e-03 2.78e+04 3.35e+00 bond pdb=" C8 G F 18 " pdb=" N7 G F 18 " ideal model delta sigma weight residual 1.305 1.294 0.011 6.00e-03 2.78e+04 3.09e+00 bond pdb=" N7 G E 18 " pdb=" C5 G E 18 " ideal model delta sigma weight residual 1.388 1.378 0.010 6.00e-03 2.78e+04 2.89e+00 bond pdb=" C4' G F 18 " pdb=" C3' G F 18 " ideal model delta sigma weight residual 1.521 1.538 -0.017 1.00e-02 1.00e+04 2.77e+00 ... (remaining 7417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 10205 1.66 - 3.32: 461 3.32 - 4.98: 27 4.98 - 6.64: 4 6.64 - 8.30: 5 Bond angle restraints: 10702 Sorted by residual: angle pdb=" O4' G E 50 " pdb=" C1' G E 50 " pdb=" N9 G E 50 " ideal model delta sigma weight residual 108.50 113.01 -4.51 7.00e-01 2.04e+00 4.14e+01 angle pdb=" C1' G E 18 " pdb=" N9 G E 18 " pdb=" C4 G E 18 " ideal model delta sigma weight residual 126.50 134.80 -8.30 1.30e+00 5.92e-01 4.08e+01 angle pdb=" O4' G F 50 " pdb=" C1' G F 50 " pdb=" N9 G F 50 " ideal model delta sigma weight residual 108.50 112.69 -4.19 7.00e-01 2.04e+00 3.59e+01 angle pdb=" C1' G E 18 " pdb=" N9 G E 18 " pdb=" C8 G E 18 " ideal model delta sigma weight residual 127.00 119.34 7.66 1.30e+00 5.92e-01 3.47e+01 angle pdb=" C1' G E 50 " pdb=" N9 G E 50 " pdb=" C8 G E 50 " ideal model delta sigma weight residual 127.00 134.65 -7.65 1.30e+00 5.92e-01 3.46e+01 ... (remaining 10697 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.65: 4217 32.65 - 65.30: 231 65.30 - 97.96: 36 97.96 - 130.61: 1 130.61 - 163.26: 3 Dihedral angle restraints: 4488 sinusoidal: 1506 harmonic: 2982 Sorted by residual: dihedral pdb=" CA GLN C 76 " pdb=" C GLN C 76 " pdb=" N VAL C 77 " pdb=" CA VAL C 77 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA GLN B 729 " pdb=" C GLN B 729 " pdb=" N LYS B 730 " pdb=" CA LYS B 730 " ideal model delta harmonic sigma weight residual 180.00 158.79 21.21 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ARG C 782 " pdb=" C ARG C 782 " pdb=" N GLU C 783 " pdb=" CA GLU C 783 " ideal model delta harmonic sigma weight residual -180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 4485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1083 0.042 - 0.084: 219 0.084 - 0.126: 169 0.126 - 0.169: 7 0.169 - 0.211: 2 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CA GLN B 729 " pdb=" N GLN B 729 " pdb=" C GLN B 729 " pdb=" CB GLN B 729 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" C1' G E 50 " pdb=" O4' G E 50 " pdb=" C2' G E 50 " pdb=" N9 G E 50 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" C1' G F 50 " pdb=" O4' G F 50 " pdb=" C2' G F 50 " pdb=" N9 G F 50 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.00e-01 ... (remaining 1477 not shown) Planarity restraints: 1118 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C E 39 " 0.044 2.00e-02 2.50e+03 2.28e-02 1.17e+01 pdb=" N1 C E 39 " -0.049 2.00e-02 2.50e+03 pdb=" C2 C E 39 " -0.009 2.00e-02 2.50e+03 pdb=" O2 C E 39 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C E 39 " 0.005 2.00e-02 2.50e+03 pdb=" C4 C E 39 " 0.006 2.00e-02 2.50e+03 pdb=" N4 C E 39 " 0.012 2.00e-02 2.50e+03 pdb=" C5 C E 39 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C E 39 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 729 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C GLN B 729 " -0.049 2.00e-02 2.50e+03 pdb=" O GLN B 729 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS B 730 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C F 38 " 0.026 2.00e-02 2.50e+03 1.35e-02 4.07e+00 pdb=" N1 C F 38 " -0.028 2.00e-02 2.50e+03 pdb=" C2 C F 38 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C F 38 " -0.005 2.00e-02 2.50e+03 pdb=" N3 C F 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C F 38 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C F 38 " 0.009 2.00e-02 2.50e+03 pdb=" C5 C F 38 " -0.004 2.00e-02 2.50e+03 pdb=" C6 C F 38 " -0.002 2.00e-02 2.50e+03 ... (remaining 1115 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 50 2.55 - 3.14: 6330 3.14 - 3.73: 12394 3.73 - 4.31: 14116 4.31 - 4.90: 20826 Nonbonded interactions: 53716 Sorted by model distance: nonbonded pdb=" O2' C F 49 " pdb=" OP1 G F 50 " model vdw 1.963 3.040 nonbonded pdb=" O2' G F 50 " pdb=" O4' A F 51 " model vdw 1.982 3.040 nonbonded pdb=" O2' U F 19 " pdb=" OP2 A F 20 " model vdw 1.988 3.040 nonbonded pdb=" O2' C E 49 " pdb=" OP1 G E 50 " model vdw 2.028 3.040 nonbonded pdb=" O2' U F 48 " pdb=" OP1 G F 50 " model vdw 2.034 3.040 ... (remaining 53711 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 5 through 81 or resid 92 through 816)) selection = (chain 'D' and resid 5 through 816) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.320 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 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 : 0.002 0.019 7422 Z= 0.231 Angle : 0.722 8.302 10702 Z= 0.635 Chirality : 0.046 0.211 1480 Planarity : 0.002 0.028 1118 Dihedral : 20.686 163.261 2524 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.07 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1008 helix: -0.28 (0.20), residues: 575 sheet: -1.29 (0.59), residues: 61 loop : -0.38 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.23 ( 7422) covalent geometry : angle 0.72247 / 0.63 (10702) hydrogen bonds : bond 0.21050 / 16.27 ( 580) hydrogen bonds : angle 7.62260 / 5.86 ( 1571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.253 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0330 time to fit residues: 2.2107 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 50.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.2980 chunk 100 optimal weight: 50.0000 chunk 106 optimal weight: 20.0000 overall best weight: 9.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.079794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.060861 restraints weight = 60394.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.060977 restraints weight = 41975.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.061264 restraints weight = 35640.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.061741 restraints weight = 29634.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.061756 restraints weight = 27948.032| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7422 Z= 0.391 Angle : 0.887 10.582 10702 Z= 0.532 Chirality : 0.058 0.419 1480 Planarity : 0.006 0.025 1118 Dihedral : 20.953 170.899 2524 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.24), residues: 1008 helix: -0.85 (0.18), residues: 638 sheet: -2.01 (0.61), residues: 55 loop : -1.22 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.39 ( 7422) covalent geometry : angle 0.88706 / 0.53 (10702) hydrogen bonds : bond 0.09936 / 7.59 ( 580) hydrogen bonds : angle 6.51942 / 5.09 ( 1571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.196 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0308 time to fit residues: 2.0766 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 111 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 76 optimal weight: 50.0000 chunk 22 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.080441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.059784 restraints weight = 58741.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.061098 restraints weight = 39202.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.062090 restraints weight = 29012.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.062609 restraints weight = 23613.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.063052 restraints weight = 20539.563| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7422 Z= 0.225 Angle : 0.613 6.931 10702 Z= 0.381 Chirality : 0.045 0.380 1480 Planarity : 0.003 0.020 1118 Dihedral : 20.844 168.965 2524 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.25), residues: 1008 helix: 0.32 (0.19), residues: 638 sheet: -2.14 (0.61), residues: 55 loop : -1.05 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.23 ( 7422) covalent geometry : angle 0.61298 / 0.38 (10702) hydrogen bonds : bond 0.06352 / 4.89 ( 580) hydrogen bonds : angle 5.44820 / 4.23 ( 1571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0303 time to fit residues: 2.0338 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 67 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 chunk 100 optimal weight: 40.0000 chunk 48 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.079821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.059131 restraints weight = 59650.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.060477 restraints weight = 38672.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.061237 restraints weight = 28166.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.062097 restraints weight = 22860.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.062415 restraints weight = 19820.887| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 7422 Z= 0.227 Angle : 0.623 8.013 10702 Z= 0.377 Chirality : 0.047 0.401 1480 Planarity : 0.003 0.020 1118 Dihedral : 20.747 175.230 2524 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.26), residues: 1008 helix: 0.82 (0.20), residues: 641 sheet: -2.08 (0.65), residues: 47 loop : -0.90 (0.36), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.23 ( 7422) covalent geometry : angle 0.62316 / 0.38 (10702) hydrogen bonds : bond 0.06726 / 5.15 ( 580) hydrogen bonds : angle 5.32706 / 4.16 ( 1571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0345 time to fit residues: 2.3128 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 30.0000 chunk 75 optimal weight: 7.9990 chunk 88 optimal weight: 0.0570 chunk 28 optimal weight: 60.0000 chunk 16 optimal weight: 9.9990 chunk 76 optimal weight: 40.0000 chunk 50 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 87 optimal weight: 5.9990 chunk 41 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 overall best weight: 6.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.078197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.059608 restraints weight = 60162.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.059872 restraints weight = 42210.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.060027 restraints weight = 36667.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.060334 restraints weight = 30753.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.060462 restraints weight = 30269.554| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7422 Z= 0.283 Angle : 0.704 9.370 10702 Z= 0.431 Chirality : 0.050 0.368 1480 Planarity : 0.004 0.019 1118 Dihedral : 21.272 174.973 2524 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.25), residues: 1008 helix: -0.09 (0.19), residues: 634 sheet: -2.66 (0.60), residues: 47 loop : -1.26 (0.36), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.28 ( 7422) covalent geometry : angle 0.70446 / 0.43 (10702) hydrogen bonds : bond 0.07291 / 5.57 ( 580) hydrogen bonds : angle 5.99422 / 4.70 ( 1571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0331 time to fit residues: 2.1919 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 105 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 29 optimal weight: 50.0000 chunk 13 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 44 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.078387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.059460 restraints weight = 59648.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.059409 restraints weight = 43722.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.059823 restraints weight = 37262.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.060248 restraints weight = 31054.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.060320 restraints weight = 29926.075| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7422 Z= 0.238 Angle : 0.633 7.228 10702 Z= 0.388 Chirality : 0.047 0.390 1480 Planarity : 0.003 0.017 1118 Dihedral : 21.129 173.173 2524 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.26), residues: 1008 helix: 0.27 (0.20), residues: 636 sheet: -2.60 (0.63), residues: 47 loop : -1.18 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.24 ( 7422) covalent geometry : angle 0.63282 / 0.39 (10702) hydrogen bonds : bond 0.06578 / 5.06 ( 580) hydrogen bonds : angle 5.63587 / 4.41 ( 1571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.224 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0322 time to fit residues: 2.1560 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 54 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 28 optimal weight: 40.0000 chunk 25 optimal weight: 2.9990 chunk 32 optimal weight: 50.0000 chunk 21 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 109 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.077799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.057477 restraints weight = 60540.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.058854 restraints weight = 39179.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.059828 restraints weight = 28538.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.060406 restraints weight = 23321.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.060654 restraints weight = 20262.307| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7422 Z= 0.248 Angle : 0.654 9.227 10702 Z= 0.397 Chirality : 0.048 0.326 1480 Planarity : 0.004 0.017 1118 Dihedral : 21.279 176.600 2524 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.26), residues: 1008 helix: 0.30 (0.20), residues: 634 sheet: -2.92 (0.60), residues: 47 loop : -1.36 (0.37), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.25 ( 7422) covalent geometry : angle 0.65434 / 0.40 (10702) hydrogen bonds : bond 0.06738 / 5.17 ( 580) hydrogen bonds : angle 5.77175 / 4.52 ( 1571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.138 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0310 time to fit residues: 2.0470 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 44 optimal weight: 20.0000 chunk 37 optimal weight: 30.0000 chunk 49 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 102 optimal weight: 20.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.078606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.058288 restraints weight = 59745.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.059711 restraints weight = 39027.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.060489 restraints weight = 29260.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.061135 restraints weight = 24027.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.061409 restraints weight = 20968.755| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7422 Z= 0.182 Angle : 0.550 6.404 10702 Z= 0.340 Chirality : 0.043 0.321 1480 Planarity : 0.003 0.015 1118 Dihedral : 21.098 174.092 2524 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.27), residues: 1008 helix: 0.91 (0.20), residues: 630 sheet: -2.94 (0.59), residues: 47 loop : -1.18 (0.36), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.18 ( 7422) covalent geometry : angle 0.54969 / 0.34 (10702) hydrogen bonds : bond 0.05777 / 4.46 ( 580) hydrogen bonds : angle 5.29920 / 4.15 ( 1571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.226 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0246 time to fit residues: 1.6740 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 29 optimal weight: 50.0000 chunk 11 optimal weight: 7.9990 chunk 48 optimal weight: 20.0000 chunk 31 optimal weight: 40.0000 chunk 15 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 19 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.076384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.056438 restraints weight = 60172.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.057607 restraints weight = 41473.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.058255 restraints weight = 31674.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.058450 restraints weight = 26375.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.058450 restraints weight = 24026.981| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7422 Z= 0.360 Angle : 0.829 15.310 10702 Z= 0.491 Chirality : 0.054 0.312 1480 Planarity : 0.005 0.021 1118 Dihedral : 21.695 179.607 2524 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.13 % Favored : 90.87 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.25), residues: 1008 helix: -0.61 (0.19), residues: 638 sheet: -3.24 (0.58), residues: 47 loop : -1.82 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.36 ( 7422) covalent geometry : angle 0.82907 / 0.49 (10702) hydrogen bonds : bond 0.08676 / 6.62 ( 580) hydrogen bonds : angle 6.54377 / 5.16 ( 1571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.134 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0246 time to fit residues: 1.6661 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 36 optimal weight: 0.0970 chunk 76 optimal weight: 40.0000 chunk 82 optimal weight: 50.0000 chunk 67 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 57 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 overall best weight: 7.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.076790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.056739 restraints weight = 60258.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.057973 restraints weight = 40694.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.058639 restraints weight = 30809.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.059283 restraints weight = 25931.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.059583 restraints weight = 22619.263| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.6169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7422 Z= 0.295 Angle : 0.713 8.150 10702 Z= 0.429 Chirality : 0.050 0.334 1480 Planarity : 0.004 0.016 1118 Dihedral : 21.507 174.594 2524 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.26), residues: 1008 helix: -0.36 (0.19), residues: 624 sheet: -3.35 (0.58), residues: 47 loop : -1.61 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.29 ( 7422) covalent geometry : angle 0.71254 / 0.43 (10702) hydrogen bonds : bond 0.07310 / 5.62 ( 580) hydrogen bonds : angle 6.18058 / 4.86 ( 1571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.228 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0304 time to fit residues: 2.0366 Evaluate side-chains 31 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 40.0000 chunk 37 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 28 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.077214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.056990 restraints weight = 60268.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.058339 restraints weight = 39543.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.059177 restraints weight = 29066.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.059651 restraints weight = 23627.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.060230 restraints weight = 20829.588| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7422 Z= 0.243 Angle : 0.628 7.184 10702 Z= 0.381 Chirality : 0.046 0.317 1480 Planarity : 0.003 0.017 1118 Dihedral : 21.364 175.249 2524 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.27), residues: 1008 helix: 0.20 (0.20), residues: 622 sheet: -3.36 (0.57), residues: 47 loop : -1.43 (0.37), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 698 PHE 0.000 0.000 PHE C 16 TRP 0.000 0.000 TRP C 522 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.24 ( 7422) covalent geometry : angle 0.62844 / 0.38 (10702) hydrogen bonds : bond 0.06600 / 5.10 ( 580) hydrogen bonds : angle 5.79814 / 4.55 ( 1571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.68 seconds wall clock time: 28 minutes 20.95 seconds (1700.95 seconds total)