Starting phenix.real_space_refine on Thu Jul 2 06:50:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rw9_54304/07_2026/9rw9_54304.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rw9_54304/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9rw9_54304/07_2026/9rw9_54304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rw9_54304/07_2026/9rw9_54304.map" model { file = "/net/cci-nas-00/data/ceres_data/9rw9_54304/07_2026/9rw9_54304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rw9_54304/07_2026/9rw9_54304.cif" } 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-dev-6108/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: 1.41, per 1000 atoms: 0.20 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: 0.49 Conformation dependent library (CDL) restraints added in 257.7 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: 0.54 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: 1.00 Time building geometry restraints manager: 0.57 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=" N1 G E 50 " pdb=" C2 G E 50 " ideal model delta sigma weight residual 1.373 1.360 0.013 8.00e-03 1.56e+04 2.73e+00 ... (remaining 7417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 10444 1.66 - 3.32: 223 3.32 - 4.98: 26 4.98 - 6.64: 4 6.64 - 8.30: 5 Bond angle restraints: 10702 Sorted by residual: 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=" 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 angle pdb=" N7 G E 50 " pdb=" C5 G E 50 " pdb=" C6 G E 50 " ideal model delta sigma weight residual 130.40 133.91 -3.51 6.00e-01 2.78e+00 3.43e+01 angle pdb=" N9 G E 50 " pdb=" C4 G E 50 " pdb=" C5 G E 50 " ideal model delta sigma weight residual 105.40 107.64 -2.24 4.00e-01 6.25e+00 3.13e+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: 1177 0.042 - 0.084: 216 0.084 - 0.126: 81 0.126 - 0.169: 5 0.169 - 0.211: 1 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 2.46 2.30 0.16 2.00e-01 2.50e+01 6.33e-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 2.46 2.30 0.15 2.00e-01 2.50e+01 5.93e-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: 2.950 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.460 Find NCS groups from input model: 0.120 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.630 ------------------------------------------------------------------------------- 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= 0.214 Angle : 0.643 8.302 10702 Z= 0.549 Chirality : 0.038 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 0.00229 / 0.21 ( 7422) covalent geometry : angle 0.64344 / 0.55 (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 : 0.173 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0246 time to fit residues: 1.6159 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=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 9.9990 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: 7.4590 ------------------------------------------------------------------------------- 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 = 0.080561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.059638 restraints weight = 59964.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.061050 restraints weight = 39093.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.061852 restraints weight = 29020.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.062528 restraints weight = 23712.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.062818 restraints weight = 20496.648| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 7422 Z= 0.336 Angle : 0.770 7.983 10702 Z= 0.489 Chirality : 0.053 0.356 1480 Planarity : 0.005 0.023 1118 Dihedral : 20.781 175.303 2524 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % 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: -0.89 (0.25), residues: 1008 helix: -0.18 (0.19), residues: 629 sheet: -1.85 (0.61), residues: 55 loop : -0.89 (0.35), residues: 324 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 0.00468 / 0.34 ( 7422) covalent geometry : angle 0.76995 / 0.49 (10702) hydrogen bonds : bond 0.08540 / 6.52 ( 580) hydrogen bonds : angle 6.07402 / 4.72 ( 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 : 0.221 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0308 time to fit residues: 2.0459 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 : 0.141 ------------------------------------------------------------------------------- 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: 8.9990 chunk 0 optimal weight: 50.0000 chunk 111 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 73 optimal weight: 30.0000 chunk 27 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 50.0000 chunk 22 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.078522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.058665 restraints weight = 59637.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.059151 restraints weight = 45163.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.060022 restraints weight = 32909.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.060418 restraints weight = 26727.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.060938 restraints weight = 23484.652| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 7422 Z= 0.329 Angle : 0.712 9.608 10702 Z= 0.462 Chirality : 0.051 0.318 1480 Planarity : 0.004 0.023 1118 Dihedral : 21.325 174.887 2524 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % 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: -1.52 (0.24), residues: 1008 helix: -0.57 (0.18), residues: 640 sheet: -2.43 (0.59), residues: 49 loop : -1.38 (0.35), residues: 319 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 0.00456 / 0.33 ( 7422) covalent geometry : angle 0.71218 / 0.46 (10702) hydrogen bonds : bond 0.08282 / 6.32 ( 580) hydrogen bonds : angle 6.21724 / 4.86 ( 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 : 0.179 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0293 time to fit residues: 1.9383 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 : 0.257 ------------------------------------------------------------------------------- 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: 0.0270 chunk 67 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 72 optimal weight: 30.0000 chunk 105 optimal weight: 9.9990 chunk 64 optimal weight: 0.0670 chunk 100 optimal weight: 40.0000 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.081441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.062744 restraints weight = 58964.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.062816 restraints weight = 39640.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.063392 restraints weight = 31786.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.063647 restraints weight = 25468.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.063823 restraints weight = 25267.365| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7422 Z= 0.125 Angle : 0.495 6.518 10702 Z= 0.322 Chirality : 0.041 0.321 1480 Planarity : 0.003 0.015 1118 Dihedral : 20.798 168.426 2524 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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 (0.27), residues: 1008 helix: 1.40 (0.20), residues: 637 sheet: -2.07 (0.65), residues: 47 loop : -0.89 (0.35), residues: 324 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 0.00174 / 0.13 ( 7422) covalent geometry : angle 0.49519 / 0.32 (10702) hydrogen bonds : bond 0.04994 / 3.85 ( 580) hydrogen bonds : angle 4.83009 / 3.75 ( 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 : 0.153 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0292 time to fit residues: 1.9391 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 40.0000 chunk 75 optimal weight: 9.9990 chunk 88 optimal weight: 30.0000 chunk 28 optimal weight: 70.0000 chunk 16 optimal weight: 9.9990 chunk 76 optimal weight: 20.0000 chunk 50 optimal weight: 10.0000 chunk 37 optimal weight: 40.0000 chunk 87 optimal weight: 6.9990 chunk 41 optimal weight: 40.0000 chunk 81 optimal weight: 6.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.078143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.059740 restraints weight = 60264.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.059338 restraints weight = 43346.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.059627 restraints weight = 38459.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.060125 restraints weight = 32298.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.060124 restraints weight = 29868.941| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 7422 Z= 0.393 Angle : 0.736 11.953 10702 Z= 0.475 Chirality : 0.053 0.315 1480 Planarity : 0.004 0.019 1118 Dihedral : 21.209 179.346 2524 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % 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: -0.86 (0.25), residues: 1008 helix: -0.05 (0.19), residues: 639 sheet: -2.47 (0.63), residues: 47 loop : -1.07 (0.36), residues: 322 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 0.00548 / 0.39 ( 7422) covalent geometry : angle 0.73614 / 0.47 (10702) hydrogen bonds : bond 0.07865 / 6.00 ( 580) hydrogen bonds : angle 6.08436 / 4.77 ( 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 : 0.136 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0280 time to fit residues: 1.8285 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 : 0.202 ------------------------------------------------------------------------------- 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: 0.9990 chunk 50 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 29 optimal weight: 50.0000 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 106 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 = 0.078111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.058773 restraints weight = 60091.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.059235 restraints weight = 43260.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.060423 restraints weight = 35625.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.060326 restraints weight = 32912.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.060308 restraints weight = 25672.560| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7422 Z= 0.300 Angle : 0.644 7.395 10702 Z= 0.421 Chirality : 0.047 0.330 1480 Planarity : 0.004 0.015 1118 Dihedral : 21.336 172.919 2524 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % 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: -0.74 (0.26), residues: 1008 helix: 0.17 (0.20), residues: 633 sheet: -2.66 (0.63), residues: 47 loop : -1.26 (0.36), residues: 328 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 0.00416 / 0.30 ( 7422) covalent geometry : angle 0.64406 / 0.42 (10702) hydrogen bonds : bond 0.06411 / 4.94 ( 580) hydrogen bonds : angle 5.78991 / 4.53 ( 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 : 0.136 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0218 time to fit residues: 1.4962 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 : 0.258 ------------------------------------------------------------------------------- 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: 6.9990 chunk 63 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 21 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 = 0.3900 r_free = 0.3900 target = 0.077192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.056927 restraints weight = 61093.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.058235 restraints weight = 40236.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.059071 restraints weight = 29999.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.059739 restraints weight = 24513.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.060045 restraints weight = 21222.569| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7422 Z= 0.309 Angle : 0.691 12.138 10702 Z= 0.444 Chirality : 0.050 0.343 1480 Planarity : 0.004 0.018 1118 Dihedral : 21.539 179.759 2524 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 15.00 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: -1.22 (0.26), residues: 1008 helix: -0.17 (0.19), residues: 639 sheet: -2.94 (0.62), residues: 47 loop : -1.56 (0.36), residues: 322 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 0.00432 / 0.31 ( 7422) covalent geometry : angle 0.69106 / 0.44 (10702) hydrogen bonds : bond 0.07656 / 5.86 ( 580) hydrogen bonds : angle 6.14589 / 4.82 ( 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 : 0.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0283 time to fit residues: 1.8803 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 : 0.168 ------------------------------------------------------------------------------- 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: 9.9990 chunk 108 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 78 optimal weight: 40.0000 chunk 44 optimal weight: 20.0000 chunk 37 optimal weight: 40.0000 chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 99 optimal weight: 0.0170 chunk 51 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 overall best weight: 2.2024 ------------------------------------------------------------------------------- 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 = 0.3952 r_free = 0.3952 target = 0.079425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.059065 restraints weight = 59462.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.060515 restraints weight = 37780.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.061550 restraints weight = 27404.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.062108 restraints weight = 21669.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.062344 restraints weight = 18712.678| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.5237 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= 0.147 Angle : 0.496 6.186 10702 Z= 0.325 Chirality : 0.042 0.316 1480 Planarity : 0.002 0.013 1118 Dihedral : 21.196 171.620 2524 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: 0.36 (0.27), residues: 1008 helix: 1.22 (0.20), residues: 639 sheet: -2.93 (0.62), residues: 47 loop : -1.20 (0.37), residues: 322 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 0.00205 / 0.15 ( 7422) covalent geometry : angle 0.49585 / 0.33 (10702) hydrogen bonds : bond 0.05172 / 4.01 ( 580) hydrogen bonds : angle 5.06790 / 3.95 ( 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 : 0.150 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0280 time to fit residues: 1.8207 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 : 0.211 ------------------------------------------------------------------------------- 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: 30.0000 chunk 15 optimal weight: 0.5980 chunk 17 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 2 optimal weight: 20.0000 chunk 86 optimal weight: 20.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.077721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.059077 restraints weight = 59544.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.059201 restraints weight = 41983.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.059456 restraints weight = 33483.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.059731 restraints weight = 28536.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.059891 restraints weight = 28225.175| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7422 Z= 0.265 Angle : 0.606 10.294 10702 Z= 0.391 Chirality : 0.046 0.296 1480 Planarity : 0.003 0.016 1118 Dihedral : 21.423 179.771 2524 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % 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: -0.45 (0.27), residues: 1008 helix: 0.49 (0.20), residues: 634 sheet: -3.11 (0.59), residues: 47 loop : -1.28 (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 0.00373 / 0.27 ( 7422) covalent geometry : angle 0.60605 / 0.39 (10702) hydrogen bonds : bond 0.06680 / 5.12 ( 580) hydrogen bonds : angle 5.65835 / 4.44 ( 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 : 0.124 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0236 time to fit residues: 1.5575 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 : 0.204 ------------------------------------------------------------------------------- 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: 20.0000 chunk 36 optimal weight: 50.0000 chunk 76 optimal weight: 50.0000 chunk 82 optimal weight: 50.0000 chunk 67 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 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 = 0.3878 r_free = 0.3878 target = 0.076072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.056192 restraints weight = 60712.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.057273 restraints weight = 43440.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.057925 restraints weight = 32807.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.058503 restraints weight = 27153.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.059004 restraints weight = 23391.448| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.6203 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= 0.384 Angle : 0.789 14.443 10702 Z= 0.502 Chirality : 0.054 0.310 1480 Planarity : 0.005 0.021 1118 Dihedral : 21.908 179.805 2524 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % 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 : 0.10 % 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: -2.10 (0.25), residues: 1008 helix: -0.81 (0.19), residues: 631 sheet: -2.99 (0.78), residues: 32 loop : -2.13 (0.34), residues: 345 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 0.00536 / 0.38 ( 7422) covalent geometry : angle 0.78880 / 0.50 (10702) hydrogen bonds : bond 0.08740 / 6.68 ( 580) hydrogen bonds : angle 6.73146 / 5.31 ( 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 : 0.220 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.0243 time to fit residues: 1.7087 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 : 0.157 ------------------------------------------------------------------------------- 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: 5.9990 chunk 79 optimal weight: 40.0000 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 0.0980 chunk 37 optimal weight: 30.0000 chunk 52 optimal weight: 0.0980 chunk 72 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 28 optimal weight: 50.0000 overall best weight: 4.8386 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.077322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.058740 restraints weight = 60284.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.058919 restraints weight = 43745.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.059313 restraints weight = 34829.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.059536 restraints weight = 29408.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.059685 restraints weight = 29014.147| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.6146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7422 Z= 0.224 Angle : 0.587 6.876 10702 Z= 0.382 Chirality : 0.046 0.317 1480 Planarity : 0.003 0.016 1118 Dihedral : 21.649 174.593 2524 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % 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: -1.07 (0.26), residues: 1008 helix: 0.00 (0.20), residues: 626 sheet: -3.42 (0.59), residues: 44 loop : -1.51 (0.37), residues: 338 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 0.00313 / 0.22 ( 7422) covalent geometry : angle 0.58705 / 0.38 (10702) hydrogen bonds : bond 0.06359 / 4.91 ( 580) hydrogen bonds : angle 5.87450 / 4.61 ( 1571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1456.84 seconds wall clock time: 25 minutes 30.46 seconds (1530.46 seconds total)