Starting phenix.real_space_refine on Thu Jul 2 08:43:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rwb_54306/07_2026/9rwb_54306.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rwb_54306/07_2026/9rwb_54306.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rwb_54306/07_2026/9rwb_54306.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rwb_54306/07_2026/9rwb_54306.map" model { file = "/net/cci-nas-00/data/ceres_data/9rwb_54306/07_2026/9rwb_54306.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rwb_54306/07_2026/9rwb_54306.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 35 5.16 5 C 4512 2.51 5 N 1324 2.21 5 O 1763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s 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: 7731 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 417 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 52} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 1216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1216 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 147} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3618 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 442} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2066 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 43, 'rna3p_pyr': 52} Link IDs: {'rna2p': 3, 'rna3p': 94} Chain breaks: 2 Time building chain proxies: 1.50, per 1000 atoms: 0.19 Number of scatterers: 7731 At special positions: 0 Unit cell: (77.307, 93.192, 154.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 97 15.00 O 1763 8.00 N 1324 7.00 C 4512 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: 0.54 Conformation dependent library (CDL) restraints added in 324.2 milliseconds 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 71.3% alpha, 9.1% beta 36 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 695 through 747 Processing helix chain 'B' and resid 696 through 747 Processing helix chain 'C' and resid 6 through 25 removed outlier: 3.692A pdb=" N LYS C 24 " --> pdb=" O ARG C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 53 through 63 Processing helix chain 'C' and resid 95 through 112 removed outlier: 3.604A pdb=" N GLU C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY C 112 " --> pdb=" O MET C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 125 removed outlier: 3.831A pdb=" N HIS C 125 " --> pdb=" O SER C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 137 Processing helix chain 'C' and resid 140 through 152 Processing helix chain 'D' and resid 4 through 25 removed outlier: 4.054A pdb=" N LYS D 24 " --> pdb=" O ARG D 20 " (cutoff:3.500A) 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 51 Processing helix chain 'D' and resid 53 through 63 Processing helix chain 'D' and resid 95 through 110 Processing helix chain 'D' and resid 119 through 125 removed outlier: 3.917A pdb=" N HIS D 125 " --> pdb=" O SER D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 140 through 152 removed outlier: 3.774A pdb=" N HIS D 151 " --> pdb=" O PHE D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 529 Processing helix chain 'D' and resid 535 through 554 Processing helix chain 'D' and resid 594 through 600 removed outlier: 3.767A 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 617 through 630 removed outlier: 4.673A pdb=" N ASP D 621 " --> pdb=" O ASP D 617 " (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 671 Processing helix chain 'D' and resid 676 through 688 removed outlier: 3.853A pdb=" N GLN D 680 " --> pdb=" O PRO D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 693 removed outlier: 4.225A pdb=" N TRP D 692 " --> pdb=" O GLN D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 698 through 714 removed outlier: 3.767A pdb=" N ASP D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) Processing helix chain 'D' and resid 714 through 725 removed outlier: 3.933A pdb=" N GLN D 724 " --> pdb=" O ASN D 720 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE D 725 " --> pdb=" O LEU D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 743 removed outlier: 3.658A pdb=" N ALA D 731 " --> pdb=" O PRO D 727 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU D 732 " --> pdb=" O GLU D 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 773 removed outlier: 3.666A pdb=" N VAL D 750 " --> pdb=" O LYS D 746 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR D 773 " --> pdb=" O LYS D 769 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 787 removed outlier: 3.579A pdb=" N ARG D 785 " --> pdb=" O ASN D 781 " (cutoff:3.500A) Processing helix chain 'D' and resid 793 through 802 removed outlier: 4.199A pdb=" N GLY D 802 " --> pdb=" O GLU D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 803 through 815 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 116 through 117 Processing sheet with id=AA3, first strand: chain 'D' and resid 28 through 29 Processing sheet with id=AA4, first strand: chain 'D' and resid 155 through 158 Processing sheet with id=AA5, first strand: chain 'D' and resid 530 through 533 removed outlier: 6.948A pdb=" N GLU D 563 " --> pdb=" O THR D 574 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 530 through 533 removed outlier: 6.573A pdb=" N ILE D 556 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N VAL D 614 " --> pdb=" O ILE D 556 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL D 558 " --> pdb=" O VAL D 614 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE D 637 " --> pdb=" O VAL D 611 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS D 613 " --> pdb=" O PHE D 637 " (cutoff:3.500A) 382 hydrogen bonds defined for protein. 1110 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 162 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 1.04 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1363 1.33 - 1.45: 2394 1.45 - 1.57: 4043 1.57 - 1.70: 192 1.70 - 1.82: 58 Bond restraints: 8050 Sorted by residual: bond pdb=" C VAL C 75 " pdb=" O VAL C 75 " ideal model delta sigma weight residual 1.236 1.207 0.028 1.01e-02 9.80e+03 7.91e+00 bond pdb=" C TYR C 74 " pdb=" N VAL C 75 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.35e-02 5.49e+03 7.54e+00 bond pdb=" CB VAL D 133 " pdb=" CG2 VAL D 133 " ideal model delta sigma weight residual 1.521 1.436 0.085 3.30e-02 9.18e+02 6.57e+00 bond pdb=" N CYS A 695 " pdb=" CA CYS A 695 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.90e-02 2.77e+03 3.93e+00 bond pdb=" CB GLN D 610 " pdb=" CG GLN D 610 " ideal model delta sigma weight residual 1.520 1.571 -0.051 3.00e-02 1.11e+03 2.92e+00 ... (remaining 8045 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 10292 1.76 - 3.51: 906 3.51 - 5.27: 85 5.27 - 7.03: 20 7.03 - 8.79: 4 Bond angle restraints: 11307 Sorted by residual: angle pdb=" O3' A E 94 " pdb=" C3' A E 94 " pdb=" C2' A E 94 " ideal model delta sigma weight residual 113.70 120.14 -6.44 1.50e+00 4.44e-01 1.84e+01 angle pdb=" C1' G E 102 " pdb=" N9 G E 102 " pdb=" C8 G E 102 " ideal model delta sigma weight residual 127.00 132.20 -5.20 1.30e+00 5.92e-01 1.60e+01 angle pdb=" O3' C E 38 " pdb=" C3' C E 38 " pdb=" C2' C E 38 " ideal model delta sigma weight residual 109.50 115.49 -5.99 1.50e+00 4.44e-01 1.59e+01 angle pdb=" C3' C E 38 " pdb=" O3' C E 38 " pdb=" P U E 39 " ideal model delta sigma weight residual 120.20 125.95 -5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C1' G E 102 " pdb=" N9 G E 102 " pdb=" C4 G E 102 " ideal model delta sigma weight residual 126.50 121.65 4.85 1.30e+00 5.92e-01 1.39e+01 ... (remaining 11302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 4783 34.20 - 68.39: 240 68.39 - 102.59: 31 102.59 - 136.78: 3 136.78 - 170.98: 1 Dihedral angle restraints: 5058 sinusoidal: 2969 harmonic: 2089 Sorted by residual: dihedral pdb=" CA GLY D 112 " pdb=" C GLY D 112 " pdb=" N ALA D 113 " pdb=" CA ALA D 113 " ideal model delta harmonic sigma weight residual -180.00 -151.67 -28.33 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA MET D 790 " pdb=" C MET D 790 " pdb=" N ASP D 791 " pdb=" CA ASP D 791 " ideal model delta harmonic sigma weight residual 180.00 153.71 26.29 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASN C 78 " pdb=" C ASN C 78 " pdb=" N ALA C 79 " pdb=" CA ALA C 79 " ideal model delta harmonic sigma weight residual 180.00 155.29 24.71 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 5055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1145 0.082 - 0.164: 196 0.164 - 0.246: 14 0.246 - 0.328: 3 0.328 - 0.410: 2 Chirality restraints: 1360 Sorted by residual: chirality pdb=" CB VAL C 75 " pdb=" CA VAL C 75 " pdb=" CG1 VAL C 75 " pdb=" CG2 VAL C 75 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C3' A E 94 " pdb=" C4' A E 94 " pdb=" O3' A E 94 " pdb=" C2' A E 94 " both_signs ideal model delta sigma weight residual False -2.48 -2.15 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C1' G E 122 " pdb=" O4' G E 122 " pdb=" C2' G E 122 " pdb=" N9 G E 122 " both_signs ideal model delta sigma weight residual False 2.46 2.18 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1357 not shown) Planarity restraints: 1093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G E 86 " 0.020 2.00e-02 2.50e+03 3.27e-02 3.20e+01 pdb=" N9 G E 86 " -0.018 2.00e-02 2.50e+03 pdb=" C8 G E 86 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G E 86 " -0.056 2.00e-02 2.50e+03 pdb=" C5 G E 86 " 0.016 2.00e-02 2.50e+03 pdb=" C6 G E 86 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G E 86 " 0.053 2.00e-02 2.50e+03 pdb=" N1 G E 86 " -0.058 2.00e-02 2.50e+03 pdb=" C2 G E 86 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G E 86 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G E 86 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G E 86 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G E 34 " -0.026 2.00e-02 2.50e+03 2.98e-02 2.67e+01 pdb=" N9 G E 34 " 0.017 2.00e-02 2.50e+03 pdb=" C8 G E 34 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G E 34 " 0.046 2.00e-02 2.50e+03 pdb=" C5 G E 34 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G E 34 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G E 34 " -0.059 2.00e-02 2.50e+03 pdb=" N1 G E 34 " 0.048 2.00e-02 2.50e+03 pdb=" C2 G E 34 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G E 34 " -0.001 2.00e-02 2.50e+03 pdb=" N3 G E 34 " 0.003 2.00e-02 2.50e+03 pdb=" C4 G E 34 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G E 17 " -0.007 2.00e-02 2.50e+03 2.95e-02 2.61e+01 pdb=" N9 G E 17 " 0.014 2.00e-02 2.50e+03 pdb=" C8 G E 17 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G E 17 " -0.051 2.00e-02 2.50e+03 pdb=" C5 G E 17 " 0.007 2.00e-02 2.50e+03 pdb=" C6 G E 17 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G E 17 " 0.041 2.00e-02 2.50e+03 pdb=" N1 G E 17 " -0.058 2.00e-02 2.50e+03 pdb=" C2 G E 17 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G E 17 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G E 17 " -0.000 2.00e-02 2.50e+03 pdb=" C4 G E 17 " 0.049 2.00e-02 2.50e+03 ... (remaining 1090 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 3203 2.94 - 3.43: 7903 3.43 - 3.92: 13760 3.92 - 4.41: 15000 4.41 - 4.90: 22325 Nonbonded interactions: 62191 Sorted by model distance: nonbonded pdb=" C GLU D 572 " pdb=" OE1 GLU D 572 " model vdw 2.455 3.270 nonbonded pdb=" OE1 GLU D 572 " pdb=" O ILE D 573 " model vdw 2.476 3.040 nonbonded pdb=" OE2 GLU D 762 " pdb=" NH1 ARG D 782 " model vdw 2.536 3.120 nonbonded pdb=" O GLU B 697 " pdb=" OG1 THR B 700 " model vdw 2.539 3.040 nonbonded pdb=" N GLN D 610 " pdb=" OE1 GLN D 610 " model vdw 2.542 3.120 ... (remaining 62186 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 695 through 735 or (resid 736 and (name N or name CA or na \ me C or name O or name CB )) or resid 737 through 747)) selection = (chain 'B' and (resid 695 through 739 or (resid 740 and (name N or name CA or na \ me C or name O or name CB )) or resid 741 through 747)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.490 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 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 : 0.005 0.085 8050 Z= 0.306 Angle : 1.035 8.786 11307 Z= 0.706 Chirality : 0.062 0.410 1360 Planarity : 0.011 0.108 1093 Dihedral : 18.736 170.977 3702 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.57 % Allowed : 2.44 % Favored : 96.99 % Rotamer: Outliers : 0.17 % Allowed : 12.56 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.29), residues: 697 helix: -0.49 (0.21), residues: 460 sheet: -1.32 (0.96), residues: 25 loop : -0.54 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG C 20 TYR 0.053 0.007 TYR D 64 PHE 0.023 0.003 PHE D 637 TRP 0.010 0.004 TRP D 522 HIS 0.016 0.004 HIS C 140 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.31 ( 8050) covalent geometry : angle 1.03474 / 0.71 (11307) hydrogen bonds : bond 0.11791 / 7.97 ( 464) hydrogen bonds : angle 6.38360 / 4.81 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7914 (tp30) cc_final: 0.7469 (tp30) REVERT: A 746 MET cc_start: 0.4753 (mtt) cc_final: 0.3994 (ttp) REVERT: C 132 GLN cc_start: 0.7434 (mt0) cc_final: 0.7146 (mp10) REVERT: D 47 ARG cc_start: 0.8298 (ttp-170) cc_final: 0.7942 (ttt-90) REVERT: D 149 MET cc_start: 0.7993 (mmt) cc_final: 0.7792 (mmm) REVERT: D 650 GLU cc_start: 0.7844 (tt0) cc_final: 0.7418 (tm-30) REVERT: D 660 TYR cc_start: 0.8419 (m-80) cc_final: 0.8141 (m-10) REVERT: D 666 LEU cc_start: 0.7583 (tp) cc_final: 0.7365 (tt) REVERT: D 733 PHE cc_start: 0.7931 (t80) cc_final: 0.7668 (t80) REVERT: D 743 MET cc_start: 0.8999 (tpt) cc_final: 0.8688 (tpt) REVERT: D 790 MET cc_start: 0.8209 (mmm) cc_final: 0.8005 (mmm) outliers start: 1 outliers final: 1 residues processed: 128 average time/residue: 0.0790 time to fit residues: 13.7105 Evaluate side-chains 106 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 105 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 706 ASN C 98 GLN C 106 ASN D 649 GLN D 664 ASN ** D 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.183878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.122910 restraints weight = 11845.690| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.39 r_work: 0.3261 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8050 Z= 0.174 Angle : 0.645 8.395 11307 Z= 0.368 Chirality : 0.042 0.235 1360 Planarity : 0.005 0.057 1093 Dihedral : 19.178 177.071 2291 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 2.30 % Favored : 97.42 % Rotamer: Outliers : 4.30 % Allowed : 11.24 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 0.49 (0.30), residues: 697 helix: 0.85 (0.23), residues: 461 sheet: -1.10 (1.01), residues: 25 loop : -0.49 (0.41), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 799 TYR 0.030 0.002 TYR D 685 PHE 0.016 0.002 PHE C 147 TRP 0.006 0.001 TRP D 522 HIS 0.008 0.002 HIS D 714 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 8050) covalent geometry : angle 0.64512 / 0.37 (11307) hydrogen bonds : bond 0.06597 / 4.37 ( 464) hydrogen bonds : angle 4.92565 / 3.69 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7956 (tp30) cc_final: 0.7479 (tp30) REVERT: A 728 GLN cc_start: 0.8177 (mt0) cc_final: 0.7925 (mt0) REVERT: A 746 MET cc_start: 0.4521 (mtt) cc_final: 0.4200 (ttt) REVERT: C 76 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7426 (pm20) REVERT: C 132 GLN cc_start: 0.7565 (mt0) cc_final: 0.7155 (mp10) REVERT: D 47 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.7904 (ttt-90) REVERT: D 109 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7836 (tt) REVERT: D 561 ASP cc_start: 0.7485 (t0) cc_final: 0.7256 (t0) REVERT: D 572 GLU cc_start: 0.7341 (tm-30) cc_final: 0.7030 (tm-30) REVERT: D 650 GLU cc_start: 0.7893 (tt0) cc_final: 0.7553 (tm-30) REVERT: D 685 TYR cc_start: 0.6946 (m-80) cc_final: 0.6651 (m-80) REVERT: D 692 TRP cc_start: 0.8119 (m100) cc_final: 0.7905 (m100) REVERT: D 743 MET cc_start: 0.8965 (tpt) cc_final: 0.8666 (tpt) REVERT: D 790 MET cc_start: 0.8333 (mmm) cc_final: 0.8132 (mmm) outliers start: 26 outliers final: 14 residues processed: 119 average time/residue: 0.0753 time to fit residues: 12.5638 Evaluate side-chains 118 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 8 MET Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 157 VAL Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 531 THR Chi-restraints excluded: chain D residue 532 VAL Chi-restraints excluded: chain D residue 562 CYS Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 593 CYS Chi-restraints excluded: chain D residue 752 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 63 optimal weight: 0.0370 chunk 21 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.0000 chunk 7 optimal weight: 0.5980 overall best weight: 0.3262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 649 GLN D 714 HIS D 724 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.185504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126145 restraints weight = 11853.465| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.44 r_work: 0.3297 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8050 Z= 0.125 Angle : 0.530 6.614 11307 Z= 0.305 Chirality : 0.038 0.177 1360 Planarity : 0.004 0.053 1093 Dihedral : 19.181 179.572 2291 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.81 % Allowed : 13.88 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.31), residues: 697 helix: 1.45 (0.24), residues: 460 sheet: -0.73 (1.05), residues: 22 loop : -0.29 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 619 TYR 0.039 0.002 TYR D 685 PHE 0.033 0.002 PHE D 691 TRP 0.006 0.001 TRP D 522 HIS 0.005 0.001 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 ( 8050) covalent geometry : angle 0.52981 / 0.31 (11307) hydrogen bonds : bond 0.05462 / 3.60 ( 464) hydrogen bonds : angle 4.37560 / 3.29 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.240 Fit side-chains revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7964 (tp30) cc_final: 0.7423 (tp30) REVERT: A 728 GLN cc_start: 0.8161 (mt0) cc_final: 0.7911 (mt0) REVERT: A 746 MET cc_start: 0.4755 (mtt) cc_final: 0.4513 (ttp) REVERT: C 123 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7773 (tp) REVERT: C 132 GLN cc_start: 0.7543 (mt0) cc_final: 0.7148 (mp10) REVERT: C 163 MET cc_start: 0.2228 (mmm) cc_final: 0.1889 (mmm) REVERT: D 4 MET cc_start: 0.6925 (tpt) cc_final: 0.6169 (tpp) REVERT: D 109 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7778 (tt) REVERT: D 572 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6923 (tm-30) REVERT: D 586 PHE cc_start: 0.5700 (m-80) cc_final: 0.5323 (m-80) REVERT: D 650 GLU cc_start: 0.7889 (tt0) cc_final: 0.7597 (tm-30) REVERT: D 743 MET cc_start: 0.8890 (tpt) cc_final: 0.8456 (tpt) REVERT: D 780 SER cc_start: 0.8221 (m) cc_final: 0.7951 (p) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 0.0721 time to fit residues: 12.1939 Evaluate side-chains 111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 588 PHE Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 649 GLN Chi-restraints excluded: chain D residue 666 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 1 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.182966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119257 restraints weight = 12024.856| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.09 r_work: 0.3280 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8050 Z= 0.157 Angle : 0.537 6.952 11307 Z= 0.302 Chirality : 0.038 0.166 1360 Planarity : 0.004 0.053 1093 Dihedral : 19.141 178.777 2291 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.31 % Allowed : 14.21 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.36 (0.31), residues: 697 helix: 1.55 (0.24), residues: 462 sheet: -0.92 (1.02), residues: 22 loop : -0.23 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 736 TYR 0.032 0.002 TYR D 685 PHE 0.021 0.002 PHE D 691 TRP 0.007 0.001 TRP D 522 HIS 0.005 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.16 ( 8050) covalent geometry : angle 0.53700 / 0.30 (11307) hydrogen bonds : bond 0.05427 / 3.59 ( 464) hydrogen bonds : angle 4.32550 / 3.26 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 710 GLU cc_start: 0.7893 (tp30) cc_final: 0.7311 (tp30) REVERT: A 728 GLN cc_start: 0.8130 (mt0) cc_final: 0.7841 (mt0) REVERT: C 132 GLN cc_start: 0.7549 (mt0) cc_final: 0.7137 (mp10) REVERT: C 163 MET cc_start: 0.2527 (mmm) cc_final: 0.2101 (mmm) REVERT: D 4 MET cc_start: 0.6941 (tpt) cc_final: 0.6125 (tpp) REVERT: D 109 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7843 (tt) REVERT: D 586 PHE cc_start: 0.5804 (m-80) cc_final: 0.5481 (m-80) REVERT: D 650 GLU cc_start: 0.7844 (tt0) cc_final: 0.7536 (tm-30) REVERT: D 733 PHE cc_start: 0.7708 (t80) cc_final: 0.7330 (t80) REVERT: D 743 MET cc_start: 0.8825 (tpt) cc_final: 0.8355 (tpt) REVERT: D 780 SER cc_start: 0.8396 (m) cc_final: 0.8111 (p) outliers start: 20 outliers final: 16 residues processed: 108 average time/residue: 0.0711 time to fit residues: 11.1142 Evaluate side-chains 111 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 565 ILE Chi-restraints excluded: chain D residue 593 CYS Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 806 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 32 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 30.0000 chunk 49 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 26 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 649 GLN D 664 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.183443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.123717 restraints weight = 11855.269| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.35 r_work: 0.3273 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8050 Z= 0.136 Angle : 0.508 6.362 11307 Z= 0.288 Chirality : 0.037 0.161 1360 Planarity : 0.004 0.050 1093 Dihedral : 19.192 177.179 2291 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.64 % Allowed : 16.03 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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 (0.31), residues: 697 helix: 1.70 (0.24), residues: 462 sheet: -0.85 (1.01), residues: 22 loop : -0.22 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.030 0.001 TYR D 685 PHE 0.021 0.002 PHE C 147 TRP 0.007 0.001 TRP D 522 HIS 0.005 0.001 HIS C 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 8050) covalent geometry : angle 0.50819 / 0.29 (11307) hydrogen bonds : bond 0.05100 / 3.35 ( 464) hydrogen bonds : angle 4.21294 / 3.17 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 99 time to evaluate : 0.246 Fit side-chains REVERT: A 710 GLU cc_start: 0.7884 (tp30) cc_final: 0.7306 (tp30) REVERT: A 728 GLN cc_start: 0.8171 (mt0) cc_final: 0.7868 (mt0) REVERT: C 76 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7159 (pm20) REVERT: C 132 GLN cc_start: 0.7611 (mt0) cc_final: 0.7167 (mp10) REVERT: D 4 MET cc_start: 0.6973 (tpt) cc_final: 0.6147 (tpp) REVERT: D 109 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7825 (tt) REVERT: D 586 PHE cc_start: 0.5805 (m-80) cc_final: 0.5507 (m-80) REVERT: D 650 GLU cc_start: 0.7939 (tt0) cc_final: 0.7638 (tm-30) REVERT: D 743 MET cc_start: 0.8809 (tpt) cc_final: 0.8379 (tpt) REVERT: D 780 SER cc_start: 0.8432 (m) cc_final: 0.8214 (p) outliers start: 22 outliers final: 13 residues processed: 112 average time/residue: 0.0655 time to fit residues: 10.7633 Evaluate side-chains 109 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 34 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 562 CYS Chi-restraints excluded: chain D residue 588 PHE Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 806 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 706 ASN D 608 HIS D 649 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.184174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.124096 restraints weight = 11913.584| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.27 r_work: 0.3288 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8050 Z= 0.120 Angle : 0.517 13.569 11307 Z= 0.286 Chirality : 0.035 0.156 1360 Planarity : 0.004 0.049 1093 Dihedral : 19.202 175.635 2291 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.98 % Allowed : 17.52 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.69 (0.31), residues: 697 helix: 1.84 (0.24), residues: 463 sheet: -1.14 (0.96), residues: 25 loop : -0.14 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.036 0.001 TYR D 685 PHE 0.022 0.002 PHE C 147 TRP 0.006 0.001 TRP D 522 HIS 0.006 0.001 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 ( 8050) covalent geometry : angle 0.51704 / 0.29 (11307) hydrogen bonds : bond 0.04814 / 3.14 ( 464) hydrogen bonds : angle 4.10730 / 3.10 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.148 Fit side-chains REVERT: A 710 GLU cc_start: 0.7856 (tp30) cc_final: 0.7279 (tp30) REVERT: A 728 GLN cc_start: 0.8162 (mt0) cc_final: 0.7868 (mt0) REVERT: C 76 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: C 132 GLN cc_start: 0.7637 (mt0) cc_final: 0.7177 (mp10) REVERT: C 163 MET cc_start: 0.2699 (mmm) cc_final: 0.2196 (mmm) REVERT: D 4 MET cc_start: 0.6915 (tpt) cc_final: 0.6098 (tpp) REVERT: D 109 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7786 (tt) REVERT: D 566 ASN cc_start: 0.6302 (m-40) cc_final: 0.5858 (m-40) REVERT: D 650 GLU cc_start: 0.8016 (tt0) cc_final: 0.7791 (tm-30) REVERT: D 743 MET cc_start: 0.8774 (tpt) cc_final: 0.8398 (tpt) REVERT: D 780 SER cc_start: 0.8405 (m) cc_final: 0.8175 (p) outliers start: 18 outliers final: 12 residues processed: 107 average time/residue: 0.0605 time to fit residues: 9.2925 Evaluate side-chains 107 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 588 PHE Chi-restraints excluded: chain D residue 593 CYS Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 806 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 12 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 31 optimal weight: 0.0770 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 706 ASN D 140 HIS ** D 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 724 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.184209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124182 restraints weight = 11815.766| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.33 r_work: 0.3286 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8050 Z= 0.117 Angle : 0.488 6.329 11307 Z= 0.275 Chirality : 0.035 0.150 1360 Planarity : 0.003 0.048 1093 Dihedral : 19.189 174.148 2291 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.81 % Allowed : 17.69 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.90 (0.32), residues: 697 helix: 1.99 (0.24), residues: 463 sheet: -1.11 (1.02), residues: 25 loop : 0.01 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 20 TYR 0.030 0.001 TYR D 685 PHE 0.020 0.002 PHE C 147 TRP 0.006 0.001 TRP D 522 HIS 0.004 0.001 HIS D 608 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 ( 8050) covalent geometry : angle 0.48785 / 0.27 (11307) hydrogen bonds : bond 0.04659 / 3.04 ( 464) hydrogen bonds : angle 4.05410 / 3.07 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.255 Fit side-chains REVERT: A 710 GLU cc_start: 0.7822 (tp30) cc_final: 0.7176 (tp30) REVERT: A 728 GLN cc_start: 0.8159 (mt0) cc_final: 0.7862 (mt0) REVERT: B 740 MET cc_start: 0.5456 (ppp) cc_final: 0.4541 (mmm) REVERT: C 76 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: C 123 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7592 (tp) REVERT: C 132 GLN cc_start: 0.7641 (mt0) cc_final: 0.7276 (mp10) REVERT: C 163 MET cc_start: 0.2721 (mmm) cc_final: 0.2250 (mmm) REVERT: D 4 MET cc_start: 0.6937 (tpt) cc_final: 0.6123 (tpp) REVERT: D 109 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7788 (tt) REVERT: D 163 MET cc_start: 0.8072 (OUTLIER) cc_final: 0.7855 (ttp) REVERT: D 566 ASN cc_start: 0.6319 (m-40) cc_final: 0.5885 (m-40) REVERT: D 650 GLU cc_start: 0.7942 (tt0) cc_final: 0.7736 (tm-30) REVERT: D 743 MET cc_start: 0.8754 (tpt) cc_final: 0.8519 (tpt) REVERT: D 755 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8407 (tttp) outliers start: 17 outliers final: 11 residues processed: 108 average time/residue: 0.0658 time to fit residues: 10.3335 Evaluate side-chains 107 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 588 PHE Chi-restraints excluded: chain D residue 593 CYS Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 806 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 72 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 706 ASN ** D 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.184755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.125412 restraints weight = 11876.020| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.34 r_work: 0.3286 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8050 Z= 0.111 Angle : 0.482 6.932 11307 Z= 0.271 Chirality : 0.034 0.145 1360 Planarity : 0.003 0.051 1093 Dihedral : 19.188 172.900 2290 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.73 % Favored : 97.13 % Rotamer: Outliers : 2.48 % Allowed : 18.35 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.04 (0.32), residues: 697 helix: 2.08 (0.24), residues: 463 sheet: -0.99 (1.04), residues: 25 loop : 0.08 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.035 0.001 TYR D 685 PHE 0.030 0.002 PHE D 733 TRP 0.005 0.001 TRP D 522 HIS 0.002 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 8050) covalent geometry : angle 0.48196 / 0.27 (11307) hydrogen bonds : bond 0.04473 / 2.90 ( 464) hydrogen bonds : angle 4.01217 / 3.05 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.311 Fit side-chains REVERT: A 710 GLU cc_start: 0.7806 (tp30) cc_final: 0.7159 (tp30) REVERT: A 728 GLN cc_start: 0.8176 (mt0) cc_final: 0.7885 (mt0) REVERT: B 740 MET cc_start: 0.5392 (ppp) cc_final: 0.4436 (mmm) REVERT: C 108 MET cc_start: 0.7274 (mmm) cc_final: 0.7054 (mmm) REVERT: C 123 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7509 (tp) REVERT: C 132 GLN cc_start: 0.7661 (mt0) cc_final: 0.7295 (mp10) REVERT: C 163 MET cc_start: 0.2711 (mmm) cc_final: 0.2270 (mmm) REVERT: D 4 MET cc_start: 0.6978 (tpt) cc_final: 0.6190 (tpp) REVERT: D 109 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7725 (tt) REVERT: D 538 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7992 (pt0) REVERT: D 650 GLU cc_start: 0.7960 (tt0) cc_final: 0.7738 (tm-30) REVERT: D 743 MET cc_start: 0.8772 (tpt) cc_final: 0.8564 (tpt) REVERT: D 755 LYS cc_start: 0.8634 (mtpp) cc_final: 0.8418 (tttp) outliers start: 15 outliers final: 11 residues processed: 104 average time/residue: 0.0549 time to fit residues: 8.4363 Evaluate side-chains 105 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 538 GLN Chi-restraints excluded: chain D residue 588 PHE Chi-restraints excluded: chain D residue 593 CYS Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 786 LEU Chi-restraints excluded: chain D residue 806 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 70 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 77 optimal weight: 30.0000 chunk 68 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 706 ASN ** D 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.183569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.122228 restraints weight = 11818.425| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.37 r_work: 0.3259 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8050 Z= 0.132 Angle : 0.494 6.929 11307 Z= 0.276 Chirality : 0.035 0.140 1360 Planarity : 0.003 0.052 1093 Dihedral : 19.165 171.962 2290 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.87 % Favored : 96.99 % Rotamer: Outliers : 2.31 % Allowed : 18.68 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.07 (0.32), residues: 697 helix: 2.11 (0.24), residues: 461 sheet: -1.08 (1.00), residues: 25 loop : 0.10 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.031 0.001 TYR D 685 PHE 0.019 0.002 PHE C 147 TRP 0.007 0.001 TRP D 692 HIS 0.003 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 ( 8050) covalent geometry : angle 0.49359 / 0.28 (11307) hydrogen bonds : bond 0.04557 / 2.96 ( 464) hydrogen bonds : angle 4.03799 / 3.07 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.239 Fit side-chains REVERT: A 710 GLU cc_start: 0.7799 (tp30) cc_final: 0.7103 (tp30) REVERT: A 728 GLN cc_start: 0.8157 (mt0) cc_final: 0.7842 (mt0) REVERT: B 740 MET cc_start: 0.5411 (ppp) cc_final: 0.4422 (mmm) REVERT: C 108 MET cc_start: 0.7155 (mmm) cc_final: 0.6876 (mmm) REVERT: C 123 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7558 (tp) REVERT: C 132 GLN cc_start: 0.7622 (mt0) cc_final: 0.7280 (mp10) REVERT: C 163 MET cc_start: 0.2697 (mmm) cc_final: 0.2271 (mmm) REVERT: D 4 MET cc_start: 0.6916 (tpt) cc_final: 0.6130 (tpp) REVERT: D 538 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: D 650 GLU cc_start: 0.7931 (tt0) cc_final: 0.7674 (tm-30) REVERT: D 743 MET cc_start: 0.8795 (tpt) cc_final: 0.8557 (tpt) REVERT: D 755 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8442 (tttp) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.0562 time to fit residues: 8.5193 Evaluate side-chains 100 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 538 GLN Chi-restraints excluded: chain D residue 588 PHE Chi-restraints excluded: chain D residue 593 CYS Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 786 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 58 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 706 ASN C 48 GLN ** D 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.184101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.120993 restraints weight = 11906.391| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.04 r_work: 0.3311 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8050 Z= 0.117 Angle : 0.482 7.019 11307 Z= 0.269 Chirality : 0.034 0.136 1360 Planarity : 0.003 0.051 1093 Dihedral : 19.164 171.117 2290 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.73 % Favored : 97.13 % Rotamer: Outliers : 2.31 % Allowed : 18.68 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.18 (0.32), residues: 697 helix: 2.19 (0.24), residues: 461 sheet: -0.96 (0.99), residues: 25 loop : 0.15 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.033 0.001 TYR D 685 PHE 0.019 0.002 PHE C 147 TRP 0.005 0.001 TRP D 692 HIS 0.003 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 ( 8050) covalent geometry : angle 0.48186 / 0.27 (11307) hydrogen bonds : bond 0.04345 / 2.81 ( 464) hydrogen bonds : angle 3.98202 / 3.03 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1394 Ramachandran restraints generated. 697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.249 Fit side-chains REVERT: A 710 GLU cc_start: 0.7717 (tp30) cc_final: 0.7064 (tp30) REVERT: A 728 GLN cc_start: 0.8075 (mt0) cc_final: 0.7760 (mt0) REVERT: B 740 MET cc_start: 0.5369 (ppp) cc_final: 0.4425 (mmm) REVERT: C 123 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7532 (tp) REVERT: C 132 GLN cc_start: 0.7596 (mt0) cc_final: 0.7253 (mp10) REVERT: C 163 MET cc_start: 0.2590 (mmm) cc_final: 0.2212 (mmm) REVERT: D 4 MET cc_start: 0.6835 (tpt) cc_final: 0.6049 (tpp) REVERT: D 109 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7753 (tt) REVERT: D 538 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.8001 (pt0) REVERT: D 650 GLU cc_start: 0.7932 (tt0) cc_final: 0.7692 (tm-30) REVERT: D 755 LYS cc_start: 0.8635 (mtpp) cc_final: 0.8390 (tttp) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.0622 time to fit residues: 9.2907 Evaluate side-chains 101 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 127 SER Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 538 GLN Chi-restraints excluded: chain D residue 588 PHE Chi-restraints excluded: chain D residue 593 CYS Chi-restraints excluded: chain D residue 604 THR Chi-restraints excluded: chain D residue 666 LEU Chi-restraints excluded: chain D residue 786 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 41 optimal weight: 5.9990 chunk 34 optimal weight: 0.2980 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 20.0000 chunk 29 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 61 optimal weight: 0.0980 chunk 15 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.184868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.122063 restraints weight = 11856.147| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.04 r_work: 0.3326 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8050 Z= 0.105 Angle : 0.473 7.682 11307 Z= 0.265 Chirality : 0.033 0.139 1360 Planarity : 0.003 0.052 1093 Dihedral : 19.138 170.807 2290 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.73 % Favored : 97.13 % Rotamer: Outliers : 2.31 % Allowed : 18.84 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 2.21 (0.32), residues: 697 helix: 2.22 (0.24), residues: 463 sheet: -0.86 (0.98), residues: 25 loop : 0.12 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 20 TYR 0.041 0.001 TYR D 685 PHE 0.020 0.002 PHE C 147 TRP 0.006 0.001 TRP D 692 HIS 0.002 0.001 HIS D 151 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 8050) covalent geometry : angle 0.47320 / 0.26 (11307) hydrogen bonds : bond 0.04167 / 2.68 ( 464) hydrogen bonds : angle 3.91901 / 2.99 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.04 seconds wall clock time: 32 minutes 50.92 seconds (1970.92 seconds total)