Starting phenix.real_space_refine on Fri Jul 3 10:50:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ieg_35381/07_2026/8ieg_35381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ieg_35381/07_2026/8ieg_35381.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ieg_35381/07_2026/8ieg_35381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ieg_35381/07_2026/8ieg_35381.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ieg_35381/07_2026/8ieg_35381.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ieg_35381/07_2026/8ieg_35381.cif" model { file = "/net/cci-nas-00/data/ceres_data/8ieg_35381/07_2026/8ieg_35381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ieg_35381/07_2026/8ieg_35381.cif" } resolution = 3.44 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= 0.002 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: 6 Type Number sf(0) Gaussians Zn 4 6.06 5 P 294 5.49 5 S 41 5.16 5 C 7940 2.51 5 N 2632 2.21 5 O 3191 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s 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: 14102 Number of models: 1 Model: "" Number of chains: 15 Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "L" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 103} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 502 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 489 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 61} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "R" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1062 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 7, 'ASP:plan': 5, 'TYR:plan': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 93 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12259 SG CYS A 663 52.674 64.189 27.278 1.00128.54 S ATOM 12418 SG CYS A 683 55.929 65.875 27.316 1.00 99.25 S ATOM 12438 SG CYS A 686 52.822 68.039 26.747 1.00114.54 S ATOM 12142 SG CYS A 648 63.679 58.375 26.869 1.00158.80 S ATOM 12162 SG CYS A 651 66.888 56.242 27.181 1.00163.10 S ATOM 12297 SG CYS A 668 63.967 55.540 29.399 1.00132.88 S ATOM 12320 SG CYS A 671 65.726 58.563 30.102 1.00117.63 S ATOM 12748 SG CYS B 663 46.002 45.510 26.823 1.00165.19 S ATOM 12907 SG CYS B 683 45.232 42.621 24.456 1.00180.95 S ATOM 12927 SG CYS B 686 46.101 41.812 28.046 1.00190.72 S ATOM 12639 SG CYS B 648 46.524 47.106 15.051 1.00200.95 S ATOM 12659 SG CYS B 651 46.478 47.902 11.323 1.00193.03 S ATOM 12786 SG CYS B 668 44.323 50.001 13.668 1.00189.88 S ATOM 12809 SG CYS B 671 43.300 46.598 13.122 1.00200.12 S Time building chain proxies: 2.27, per 1000 atoms: 0.16 Number of scatterers: 14102 At special positions: 0 Unit cell: (120.288, 122.436, 111.696, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 4 29.99 S 41 16.00 P 294 15.00 O 3191 8.00 N 2632 7.00 C 7940 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 340.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" ND1 HIS A 665 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 683 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 663 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 686 " pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 668 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 671 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 648 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 651 " pdb=" ZN B 801 " pdb="ZN ZN B 801 " - pdb=" ND1 HIS B 665 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 683 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 663 " pdb="ZN ZN B 801 " - pdb=" SG CYS B 686 " pdb=" ZN B 802 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 671 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 668 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 651 " pdb="ZN ZN B 802 " - pdb=" SG CYS B 648 " Number of angles added : 18 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 62.9% alpha, 5.3% beta 140 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'K' and resid 44 through 55 Processing helix chain 'K' and resid 63 through 76 Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 131 removed outlier: 3.556A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 49 through 76 removed outlier: 4.127A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 removed outlier: 3.527A pdb=" N GLN L 93 " --> pdb=" O ALA L 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.557A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.470A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.535A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.539A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.504A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.533A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.635A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.601A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.777A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.406A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'A' and resid 638 through 647 Processing helix chain 'A' and resid 668 through 678 Processing helix chain 'B' and resid 639 through 647 Processing helix chain 'B' and resid 668 through 678 Processing helix chain 'B' and resid 691 through 693 No H-bonds generated for 'chain 'B' and resid 691 through 693' Processing helix chain 'R' and resid 4 through 19 Processing helix chain 'R' and resid 89 through 94 Processing helix chain 'R' and resid 101 through 115 removed outlier: 3.736A pdb=" N ASN R 114 " --> pdb=" O GLN R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 123 through 133 Processing helix chain 'R' and resid 133 through 150 Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.296A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.809A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.098A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.324A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'A' and resid 666 through 667 Processing sheet with id=AB3, first strand: chain 'B' and resid 666 through 667 Processing sheet with id=AB4, first strand: chain 'R' and resid 24 through 29 removed outlier: 3.636A pdb=" N MET R 39 " --> pdb=" O SER R 25 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER R 27 " --> pdb=" O ASN R 37 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL R 35 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU R 58 " --> pdb=" O HIS R 69 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N HIS R 69 " --> pdb=" O GLU R 58 " (cutoff:3.500A) 482 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 360 hydrogen bonds 716 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 2.43 Time building geometry restraints manager: 1.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3261 1.34 - 1.45: 4336 1.45 - 1.57: 6714 1.57 - 1.69: 586 1.69 - 1.81: 60 Bond restraints: 14957 Sorted by residual: bond pdb=" C3' DG I 21 " pdb=" C2' DG I 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DC I 30 " pdb=" C2' DC I 30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DT J 64 " pdb=" C2' DT J 64 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.86e+00 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.34e+00 ... (remaining 14952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 20333 1.60 - 3.20: 1109 3.20 - 4.80: 31 4.80 - 6.39: 9 6.39 - 7.99: 1 Bond angle restraints: 21483 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.53 108.09 5.44 9.80e-01 1.04e+00 3.08e+01 angle pdb=" N ARG R 7 " pdb=" CA ARG R 7 " pdb=" C ARG R 7 " ideal model delta sigma weight residual 111.14 106.25 4.89 1.08e+00 8.57e-01 2.05e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J 41 " pdb=" C4 DT J 41 " pdb=" O4 DT J 41 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 ... (remaining 21478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 6823 33.77 - 67.54: 1411 67.54 - 101.32: 13 101.32 - 135.09: 1 135.09 - 168.86: 3 Dihedral angle restraints: 8251 sinusoidal: 5234 harmonic: 3017 Sorted by residual: dihedral pdb=" C4' DT I -59 " pdb=" C3' DT I -59 " pdb=" O3' DT I -59 " pdb=" P DC I -58 " ideal model delta sinusoidal sigma weight residual 220.00 51.14 168.86 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 68.60 151.40 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA ILE L 29 " pdb=" C ILE L 29 " pdb=" N THR L 30 " pdb=" CA THR L 30 " ideal model delta harmonic sigma weight residual -180.00 -161.51 -18.49 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 8248 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1570 0.040 - 0.079: 670 0.079 - 0.119: 191 0.119 - 0.159: 15 0.159 - 0.198: 3 Chirality restraints: 2449 Sorted by residual: chirality pdb=" C3' DT I 15 " pdb=" C4' DT I 15 " pdb=" O3' DT I 15 " pdb=" C2' DT I 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.82e-01 chirality pdb=" CA ILE L 29 " pdb=" N ILE L 29 " pdb=" C ILE L 29 " pdb=" CB ILE L 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA GLU K 97 " pdb=" N GLU K 97 " pdb=" C GLU K 97 " pdb=" CB GLU K 97 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 2446 not shown) Planarity restraints: 1707 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 92 " -0.192 9.50e-02 1.11e+02 8.63e-02 4.72e+00 pdb=" NE ARG F 92 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG F 92 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG F 92 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG F 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 63 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO R 64 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 64 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 64 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.24e+00 pdb=" N PRO D 103 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.021 5.00e-02 4.00e+02 ... (remaining 1704 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 34 2.35 - 2.99: 6285 2.99 - 3.63: 22643 3.63 - 4.26: 37950 4.26 - 4.90: 55040 Nonbonded interactions: 121952 Sorted by model distance: nonbonded pdb=" O HIS A 699 " pdb=" O LEU A 700 " model vdw 1.714 3.040 nonbonded pdb=" OD2 ASP C 90 " pdb=" NH2 ARG A 679 " model vdw 1.941 3.120 nonbonded pdb=" CD2 LEU C 65 " pdb=" NH1 ARG A 681 " model vdw 1.965 3.540 nonbonded pdb=" CB PRO R 4 " pdb=" NH1 ARG R 7 " model vdw 2.088 3.520 nonbonded pdb=" OH TYR C 50 " pdb=" OE1 GLN D 95 " model vdw 2.109 3.040 ... (remaining 121947 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 638 through 652 or (resid 653 and (name N or name CA or na \ me C or name O or name CB )) or resid 654 through 660 or (resid 661 and (name N \ or name CA or name C or name O or name CB )) or resid 662 through 802)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 119 or resid 121 through 124)) selection = (chain 'H' and (resid 31 through 119 or resid 121 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 38 through 134) } ncs_group { reference = chain 'F' selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.007 0.455 14974 Z= 0.609 Angle : 0.749 8.875 21501 Z= 0.636 Chirality : 0.045 0.198 2449 Planarity : 0.005 0.086 1707 Dihedral : 25.787 168.858 6293 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.43 % Allowed : 1.78 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.84 (0.27), residues: 1013 helix: 1.36 (0.21), residues: 639 sheet: -1.45 (0.86), residues: 41 loop : -0.66 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 92 TYR 0.018 0.001 TYR D 40 PHE 0.016 0.002 PHE B 642 TRP 0.007 0.001 TRP R 96 HIS 0.003 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.48 (14957) covalent geometry : angle 0.74080 / 0.64 (21483) hydrogen bonds : bond 0.13474 / 9.40 ( 842) hydrogen bonds : angle 4.76814 / 3.42 ( 2144) metal coordination : bond 0.01304 / 0.72 ( 16) metal coordination : angle 3.96135 / 2.15 ( 18) Misc. bond : bond 0.45518 / 23.96 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 393 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 49 LEU cc_start: 0.8407 (mt) cc_final: 0.7814 (mm) REVERT: C 39 TYR cc_start: 0.7556 (m-80) cc_final: 0.7050 (m-80) REVERT: C 57 TYR cc_start: 0.8657 (t80) cc_final: 0.8428 (t80) REVERT: C 61 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7300 (tp30) REVERT: C 94 ASN cc_start: 0.8311 (t0) cc_final: 0.8079 (t0) REVERT: D 92 ARG cc_start: 0.7481 (ttt90) cc_final: 0.7249 (ttt90) REVERT: A 642 PHE cc_start: 0.3287 (m-10) cc_final: 0.3073 (m-10) REVERT: A 662 THR cc_start: 0.7869 (m) cc_final: 0.7514 (t) REVERT: A 669 GLU cc_start: 0.7203 (pp20) cc_final: 0.6833 (tm-30) REVERT: B 647 TYR cc_start: 0.2572 (m-80) cc_final: 0.2233 (m-80) REVERT: B 679 ARG cc_start: 0.2542 (OUTLIER) cc_final: 0.1385 (tpt90) REVERT: R 81 VAL cc_start: 0.7850 (t) cc_final: 0.7331 (t) REVERT: R 82 TYR cc_start: 0.8261 (m-80) cc_final: 0.7880 (m-80) REVERT: R 90 ASP cc_start: 0.8777 (p0) cc_final: 0.8479 (p0) REVERT: R 110 GLN cc_start: 0.2991 (OUTLIER) cc_final: 0.2362 (tt0) outliers start: 12 outliers final: 2 residues processed: 398 average time/residue: 0.1323 time to fit residues: 71.7409 Evaluate side-chains 271 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 267 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 679 ARG Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS G 73 ASN G 104 GLN A 699 HIS B 670 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.069329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.046412 restraints weight = 64465.223| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.29 r_work: 0.2747 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 14974 Z= 0.169 Angle : 0.679 8.551 21501 Z= 0.394 Chirality : 0.045 0.237 2449 Planarity : 0.005 0.063 1707 Dihedral : 29.408 170.748 4362 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.62 % Allowed : 14.51 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.91 (0.26), residues: 1013 helix: 1.42 (0.20), residues: 647 sheet: -1.58 (0.81), residues: 48 loop : -0.66 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 681 TYR 0.020 0.002 TYR H 83 PHE 0.021 0.002 PHE R 72 TRP 0.036 0.004 TRP R 149 HIS 0.012 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.17 (14957) covalent geometry : angle 0.67167 / 0.39 (21483) hydrogen bonds : bond 0.05196 / 3.41 ( 842) hydrogen bonds : angle 3.67655 / 2.68 ( 2144) metal coordination : bond 0.01697 / 0.89 ( 16) metal coordination : angle 3.45313 / 1.89 ( 18) Misc. bond : bond 0.00175 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 286 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 84 MET cc_start: 0.9469 (mmm) cc_final: 0.9148 (mmm) REVERT: C 39 TYR cc_start: 0.8654 (m-80) cc_final: 0.8371 (m-80) REVERT: D 93 GLU cc_start: 0.8792 (mp0) cc_final: 0.8454 (mp0) REVERT: G 39 TYR cc_start: 0.9150 (m-80) cc_final: 0.8621 (m-80) REVERT: G 56 GLU cc_start: 0.9236 (tt0) cc_final: 0.8822 (tt0) REVERT: G 90 ASP cc_start: 0.8584 (t0) cc_final: 0.8191 (t0) REVERT: G 92 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8239 (mt-10) REVERT: H 33 ARG cc_start: 0.5481 (mtp85) cc_final: 0.4326 (ttm170) REVERT: H 68 ASP cc_start: 0.9314 (t0) cc_final: 0.9043 (t0) REVERT: H 79 ARG cc_start: 0.9146 (ttm-80) cc_final: 0.8885 (ttm-80) REVERT: H 93 GLU cc_start: 0.8960 (mp0) cc_final: 0.8741 (mp0) REVERT: A 669 GLU cc_start: 0.8035 (pp20) cc_final: 0.7353 (tm-30) REVERT: A 674 GLU cc_start: 0.8813 (pp20) cc_final: 0.8607 (pt0) REVERT: A 680 MET cc_start: 0.8432 (ttm) cc_final: 0.8147 (ttm) REVERT: A 681 ARG cc_start: 0.8080 (mtm-85) cc_final: 0.7825 (mtm-85) REVERT: B 679 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5212 (tpt170) REVERT: R 36 TRP cc_start: 0.5903 (m100) cc_final: 0.5530 (m100) REVERT: R 72 PHE cc_start: 0.8902 (m-80) cc_final: 0.8196 (m-80) REVERT: R 90 ASP cc_start: 0.9297 (p0) cc_final: 0.9035 (p0) REVERT: R 110 GLN cc_start: 0.3173 (OUTLIER) cc_final: 0.2966 (tp40) outliers start: 22 outliers final: 13 residues processed: 298 average time/residue: 0.1097 time to fit residues: 46.5914 Evaluate side-chains 266 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 251 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain K residue 115 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain B residue 679 ARG Chi-restraints excluded: chain B residue 696 LEU Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 120 optimal weight: 6.9990 chunk 87 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 98 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 113 HIS E 68 GLN G 73 ASN G 104 GLN A 699 HIS ** R 80 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.067238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.044244 restraints weight = 65517.722| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.26 r_work: 0.2697 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 14974 Z= 0.226 Angle : 0.691 8.420 21501 Z= 0.390 Chirality : 0.044 0.229 2449 Planarity : 0.005 0.086 1707 Dihedral : 29.735 172.439 4362 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.45 % Allowed : 14.74 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.12 (0.26), residues: 1013 helix: 1.62 (0.20), residues: 646 sheet: -1.20 (0.85), residues: 47 loop : -0.71 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 54 TYR 0.043 0.002 TYR H 83 PHE 0.035 0.002 PHE R 72 TRP 0.018 0.003 TRP R 149 HIS 0.006 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.23 (14957) covalent geometry : angle 0.68069 / 0.39 (21483) hydrogen bonds : bond 0.05342 / 3.55 ( 842) hydrogen bonds : angle 3.66715 / 2.69 ( 2144) metal coordination : bond 0.01742 / 0.95 ( 16) metal coordination : angle 4.11642 / 2.51 ( 18) Misc. bond : bond 0.00180 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 258 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 44 LYS cc_start: 0.9229 (mtpt) cc_final: 0.8804 (mtpt) REVERT: L 84 MET cc_start: 0.9404 (mmm) cc_final: 0.8873 (mmm) REVERT: C 56 GLU cc_start: 0.9346 (tm-30) cc_final: 0.8883 (tm-30) REVERT: C 91 GLU cc_start: 0.8229 (pm20) cc_final: 0.7843 (pm20) REVERT: C 92 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8729 (mm-30) REVERT: D 76 GLU cc_start: 0.9101 (tp30) cc_final: 0.8821 (tp30) REVERT: D 93 GLU cc_start: 0.8967 (mp0) cc_final: 0.8619 (mp0) REVERT: F 74 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8584 (mt-10) REVERT: G 25 PHE cc_start: 0.9012 (m-80) cc_final: 0.8699 (m-80) REVERT: G 56 GLU cc_start: 0.9282 (tt0) cc_final: 0.8910 (tt0) REVERT: G 90 ASP cc_start: 0.8650 (t0) cc_final: 0.8141 (t0) REVERT: G 92 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8419 (mt-10) REVERT: H 33 ARG cc_start: 0.5279 (mtp85) cc_final: 0.5042 (mtt90) REVERT: H 46 LYS cc_start: 0.9201 (mmmt) cc_final: 0.8942 (mmmt) REVERT: H 68 ASP cc_start: 0.9394 (t0) cc_final: 0.9072 (t0) REVERT: H 93 GLU cc_start: 0.9087 (mp0) cc_final: 0.8678 (mp0) REVERT: A 655 TRP cc_start: 0.8107 (m-90) cc_final: 0.7798 (t-100) REVERT: A 669 GLU cc_start: 0.8177 (pp20) cc_final: 0.7512 (tm-30) REVERT: A 673 LYS cc_start: 0.8761 (pttt) cc_final: 0.8468 (pttp) REVERT: A 674 GLU cc_start: 0.8855 (pp20) cc_final: 0.8549 (pt0) REVERT: A 680 MET cc_start: 0.8423 (ttm) cc_final: 0.7952 (ttm) REVERT: R 72 PHE cc_start: 0.9168 (m-80) cc_final: 0.8223 (m-10) REVERT: R 90 ASP cc_start: 0.9212 (p0) cc_final: 0.8919 (p0) REVERT: R 110 GLN cc_start: 0.3308 (OUTLIER) cc_final: 0.2619 (tp40) outliers start: 29 outliers final: 20 residues processed: 274 average time/residue: 0.1182 time to fit residues: 46.1748 Evaluate side-chains 258 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN G 104 GLN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.067889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.044531 restraints weight = 65631.715| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.26 r_work: 0.2709 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14974 Z= 0.159 Angle : 0.648 11.120 21501 Z= 0.369 Chirality : 0.043 0.241 2449 Planarity : 0.005 0.057 1707 Dihedral : 29.779 171.948 4352 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.73 % Allowed : 16.77 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.26 (0.27), residues: 1013 helix: 1.74 (0.20), residues: 648 sheet: -1.35 (0.79), residues: 48 loop : -0.66 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 79 TYR 0.038 0.002 TYR H 83 PHE 0.020 0.002 PHE R 72 TRP 0.032 0.003 TRP R 36 HIS 0.016 0.001 HIS R 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (14957) covalent geometry : angle 0.63961 / 0.37 (21483) hydrogen bonds : bond 0.04503 / 2.94 ( 842) hydrogen bonds : angle 3.51944 / 2.58 ( 2144) metal coordination : bond 0.01573 / 0.87 ( 16) metal coordination : angle 3.73642 / 2.24 ( 18) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 263 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 39 HIS cc_start: 0.7394 (t70) cc_final: 0.7114 (t-90) REVERT: L 44 LYS cc_start: 0.9237 (mtpt) cc_final: 0.8629 (mtpt) REVERT: C 91 GLU cc_start: 0.8348 (pm20) cc_final: 0.7969 (pm20) REVERT: C 92 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8698 (mm-30) REVERT: D 43 LYS cc_start: 0.9709 (OUTLIER) cc_final: 0.9483 (mttp) REVERT: D 62 MET cc_start: 0.9523 (mmm) cc_final: 0.9286 (mmm) REVERT: D 76 GLU cc_start: 0.9070 (tp30) cc_final: 0.8806 (tp30) REVERT: D 93 GLU cc_start: 0.9009 (mp0) cc_final: 0.8695 (mp0) REVERT: E 77 ASP cc_start: 0.9295 (m-30) cc_final: 0.8919 (p0) REVERT: F 74 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8545 (mt-10) REVERT: G 25 PHE cc_start: 0.9006 (m-80) cc_final: 0.8736 (m-80) REVERT: G 39 TYR cc_start: 0.9378 (m-80) cc_final: 0.8783 (m-80) REVERT: G 56 GLU cc_start: 0.9303 (tt0) cc_final: 0.8950 (tt0) REVERT: G 90 ASP cc_start: 0.8627 (t0) cc_final: 0.8129 (t0) REVERT: G 92 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8538 (mt-10) REVERT: H 33 ARG cc_start: 0.5238 (mtp85) cc_final: 0.4765 (mmm160) REVERT: H 46 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8940 (mmmt) REVERT: H 68 ASP cc_start: 0.9391 (t0) cc_final: 0.9071 (t0) REVERT: H 93 GLU cc_start: 0.9099 (mp0) cc_final: 0.8670 (mp0) REVERT: A 658 MET cc_start: 0.8162 (tpp) cc_final: 0.7790 (tpt) REVERT: A 669 GLU cc_start: 0.8159 (pp20) cc_final: 0.7421 (tm-30) REVERT: A 673 LYS cc_start: 0.8733 (pttt) cc_final: 0.8413 (pttp) REVERT: A 674 GLU cc_start: 0.8881 (pp20) cc_final: 0.8553 (pt0) REVERT: A 680 MET cc_start: 0.8346 (ttm) cc_final: 0.7924 (ttm) REVERT: A 681 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8252 (mtm-85) REVERT: R 89 LEU cc_start: 0.8982 (tp) cc_final: 0.8394 (pt) REVERT: R 90 ASP cc_start: 0.9174 (p0) cc_final: 0.8900 (p0) REVERT: R 110 GLN cc_start: 0.3289 (OUTLIER) cc_final: 0.3017 (mm110) outliers start: 23 outliers final: 15 residues processed: 274 average time/residue: 0.1114 time to fit residues: 43.7347 Evaluate side-chains 261 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** R 80 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 = 0.3646 r_free = 0.3646 target = 0.068156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.044544 restraints weight = 67106.603| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.31 r_work: 0.2714 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14974 Z= 0.147 Angle : 0.642 11.424 21501 Z= 0.365 Chirality : 0.042 0.241 2449 Planarity : 0.004 0.055 1707 Dihedral : 29.774 172.146 4352 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.45 % Allowed : 18.31 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.39 (0.27), residues: 1013 helix: 1.84 (0.21), residues: 649 sheet: -1.39 (0.76), residues: 48 loop : -0.61 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 79 TYR 0.025 0.002 TYR F 88 PHE 0.035 0.002 PHE R 72 TRP 0.040 0.004 TRP R 36 HIS 0.006 0.001 HIS R 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (14957) covalent geometry : angle 0.63419 / 0.36 (21483) hydrogen bonds : bond 0.04337 / 2.83 ( 842) hydrogen bonds : angle 3.49540 / 2.57 ( 2144) metal coordination : bond 0.01325 / 0.74 ( 16) metal coordination : angle 3.46448 / 2.22 ( 18) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 256 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 39 HIS cc_start: 0.7366 (t70) cc_final: 0.7100 (t-90) REVERT: C 91 GLU cc_start: 0.8410 (pm20) cc_final: 0.8072 (pm20) REVERT: C 92 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8671 (mm-30) REVERT: D 43 LYS cc_start: 0.9702 (OUTLIER) cc_final: 0.9478 (mttp) REVERT: D 62 MET cc_start: 0.9472 (mmm) cc_final: 0.9267 (mmm) REVERT: D 76 GLU cc_start: 0.9054 (tp30) cc_final: 0.8802 (tp30) REVERT: D 93 GLU cc_start: 0.9024 (mp0) cc_final: 0.8697 (mp0) REVERT: D 105 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8163 (mm-30) REVERT: E 77 ASP cc_start: 0.9268 (m-30) cc_final: 0.8957 (p0) REVERT: F 70 VAL cc_start: 0.9366 (m) cc_final: 0.9134 (p) REVERT: F 74 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8482 (mt-10) REVERT: F 88 TYR cc_start: 0.9261 (m-10) cc_final: 0.9053 (m-10) REVERT: G 25 PHE cc_start: 0.8996 (m-80) cc_final: 0.8768 (m-80) REVERT: G 39 TYR cc_start: 0.9405 (m-80) cc_final: 0.8799 (m-80) REVERT: G 56 GLU cc_start: 0.9278 (tt0) cc_final: 0.8951 (tt0) REVERT: G 90 ASP cc_start: 0.8693 (t0) cc_final: 0.8157 (t0) REVERT: H 46 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8910 (mmmt) REVERT: H 68 ASP cc_start: 0.9374 (t0) cc_final: 0.9038 (t0) REVERT: H 93 GLU cc_start: 0.9096 (mp0) cc_final: 0.8679 (mp0) REVERT: H 101 LEU cc_start: 0.9155 (mt) cc_final: 0.8908 (mm) REVERT: A 658 MET cc_start: 0.8064 (tpp) cc_final: 0.7837 (tpp) REVERT: A 669 GLU cc_start: 0.8214 (pp20) cc_final: 0.7526 (tm-30) REVERT: A 673 LYS cc_start: 0.8735 (pttt) cc_final: 0.8417 (pttp) REVERT: A 674 GLU cc_start: 0.8948 (pp20) cc_final: 0.8596 (pt0) REVERT: A 680 MET cc_start: 0.8410 (ttm) cc_final: 0.8081 (ttm) REVERT: A 681 ARG cc_start: 0.8660 (mtm-85) cc_final: 0.8163 (mtm-85) REVERT: B 673 LYS cc_start: 0.8243 (pttp) cc_final: 0.8035 (pttm) REVERT: B 695 LEU cc_start: 0.7527 (mp) cc_final: 0.7148 (tt) REVERT: R 72 PHE cc_start: 0.8855 (m-10) cc_final: 0.7958 (m-10) REVERT: R 89 LEU cc_start: 0.8957 (tp) cc_final: 0.8359 (pt) REVERT: R 90 ASP cc_start: 0.9131 (p0) cc_final: 0.8749 (p0) outliers start: 29 outliers final: 19 residues processed: 270 average time/residue: 0.1105 time to fit residues: 42.4775 Evaluate side-chains 268 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 248 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 38 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 72 optimal weight: 40.0000 chunk 116 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 7 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 699 HIS ** R 80 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 = 0.3625 r_free = 0.3625 target = 0.066984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.043307 restraints weight = 66676.462| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.27 r_work: 0.2679 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14974 Z= 0.215 Angle : 0.672 12.153 21501 Z= 0.376 Chirality : 0.043 0.233 2449 Planarity : 0.004 0.036 1707 Dihedral : 29.929 172.917 4349 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.33 % Allowed : 19.26 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.40 (0.27), residues: 1013 helix: 1.85 (0.20), residues: 647 sheet: -1.26 (0.77), residues: 48 loop : -0.61 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.026 0.002 TYR F 88 PHE 0.020 0.002 PHE R 13 TRP 0.034 0.003 TRP R 36 HIS 0.010 0.001 HIS R 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (14957) covalent geometry : angle 0.66406 / 0.38 (21483) hydrogen bonds : bond 0.04879 / 3.24 ( 842) hydrogen bonds : angle 3.59699 / 2.64 ( 2144) metal coordination : bond 0.01716 / 0.96 ( 16) metal coordination : angle 3.54555 / 2.24 ( 18) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 243 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8512 (pm20) cc_final: 0.8153 (pm20) REVERT: C 92 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8467 (mm-30) REVERT: D 43 LYS cc_start: 0.9716 (OUTLIER) cc_final: 0.9490 (mttp) REVERT: D 76 GLU cc_start: 0.9109 (tp30) cc_final: 0.8891 (tp30) REVERT: D 93 GLU cc_start: 0.9101 (mp0) cc_final: 0.8795 (mp0) REVERT: D 105 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8411 (mm-30) REVERT: E 77 ASP cc_start: 0.9286 (m-30) cc_final: 0.9019 (p0) REVERT: E 79 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.6808 (tttt) REVERT: F 88 TYR cc_start: 0.9280 (m-10) cc_final: 0.9010 (m-10) REVERT: G 39 TYR cc_start: 0.9464 (m-80) cc_final: 0.8793 (m-80) REVERT: G 56 GLU cc_start: 0.9310 (tt0) cc_final: 0.9020 (tt0) REVERT: G 73 ASN cc_start: 0.8875 (OUTLIER) cc_final: 0.8671 (t0) REVERT: G 90 ASP cc_start: 0.8723 (t0) cc_final: 0.8218 (t0) REVERT: G 92 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8419 (tt0) REVERT: H 46 LYS cc_start: 0.9216 (mmmt) cc_final: 0.8977 (mmmt) REVERT: H 68 ASP cc_start: 0.9405 (t0) cc_final: 0.9063 (t0) REVERT: H 93 GLU cc_start: 0.9096 (mp0) cc_final: 0.8674 (mp0) REVERT: H 101 LEU cc_start: 0.9187 (mt) cc_final: 0.8967 (mm) REVERT: A 669 GLU cc_start: 0.8232 (pp20) cc_final: 0.7538 (tm-30) REVERT: A 673 LYS cc_start: 0.8732 (pttt) cc_final: 0.8481 (pttp) REVERT: A 680 MET cc_start: 0.8369 (ttm) cc_final: 0.8027 (ttm) REVERT: A 681 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8140 (mtm-85) REVERT: B 658 MET cc_start: 0.5057 (tmm) cc_final: 0.4611 (tmm) REVERT: B 695 LEU cc_start: 0.7126 (mp) cc_final: 0.6646 (tt) REVERT: R 72 PHE cc_start: 0.8735 (m-10) cc_final: 0.7891 (m-10) REVERT: R 90 ASP cc_start: 0.9204 (p0) cc_final: 0.8993 (p0) REVERT: R 129 LEU cc_start: 0.5881 (tp) cc_final: 0.5337 (mt) REVERT: R 133 HIS cc_start: 0.8509 (t-170) cc_final: 0.8308 (t-90) outliers start: 28 outliers final: 19 residues processed: 259 average time/residue: 0.1025 time to fit residues: 38.6017 Evaluate side-chains 258 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 236 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 5 optimal weight: 0.9990 chunk 110 optimal weight: 0.0980 chunk 69 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 104 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.067992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.044407 restraints weight = 66867.088| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 3.31 r_work: 0.2717 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14974 Z= 0.142 Angle : 0.642 12.102 21501 Z= 0.365 Chirality : 0.042 0.243 2449 Planarity : 0.004 0.049 1707 Dihedral : 29.849 172.028 4349 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.02 % Allowed : 21.64 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.53 (0.27), residues: 1013 helix: 1.96 (0.20), residues: 647 sheet: -1.09 (0.81), residues: 44 loop : -0.60 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.029 0.002 TYR R 100 PHE 0.018 0.002 PHE R 13 TRP 0.027 0.003 TRP R 36 HIS 0.013 0.002 HIS A 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (14957) covalent geometry : angle 0.63612 / 0.36 (21483) hydrogen bonds : bond 0.04192 / 2.70 ( 842) hydrogen bonds : angle 3.43731 / 2.52 ( 2144) metal coordination : bond 0.01298 / 0.72 ( 16) metal coordination : angle 3.15322 / 1.99 ( 18) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 253 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8532 (pm20) cc_final: 0.8188 (pm20) REVERT: C 92 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8484 (mm-30) REVERT: D 43 LYS cc_start: 0.9702 (OUTLIER) cc_final: 0.9471 (mttp) REVERT: D 76 GLU cc_start: 0.9055 (tp30) cc_final: 0.8838 (tp30) REVERT: D 93 GLU cc_start: 0.9065 (mp0) cc_final: 0.8736 (mp0) REVERT: D 105 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8180 (mm-30) REVERT: E 77 ASP cc_start: 0.9287 (m-30) cc_final: 0.9007 (p0) REVERT: F 88 TYR cc_start: 0.9246 (m-10) cc_final: 0.8948 (m-10) REVERT: G 39 TYR cc_start: 0.9425 (m-80) cc_final: 0.8791 (m-80) REVERT: G 56 GLU cc_start: 0.9335 (tt0) cc_final: 0.8989 (tt0) REVERT: G 73 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8666 (t0) REVERT: G 90 ASP cc_start: 0.8685 (t0) cc_final: 0.8063 (t0) REVERT: H 33 ARG cc_start: 0.5334 (mtp85) cc_final: 0.4862 (mmm160) REVERT: H 42 TYR cc_start: 0.8862 (t80) cc_final: 0.8569 (t80) REVERT: H 46 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8974 (mmmt) REVERT: H 68 ASP cc_start: 0.9385 (t0) cc_final: 0.9055 (t0) REVERT: H 93 GLU cc_start: 0.9109 (mp0) cc_final: 0.8663 (mp0) REVERT: H 101 LEU cc_start: 0.9167 (mt) cc_final: 0.8927 (mm) REVERT: H 105 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8691 (mm-30) REVERT: A 669 GLU cc_start: 0.8273 (pp20) cc_final: 0.7640 (tm-30) REVERT: A 673 LYS cc_start: 0.8769 (pttt) cc_final: 0.8516 (pttp) REVERT: A 680 MET cc_start: 0.8407 (ttm) cc_final: 0.8046 (ttm) REVERT: A 681 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8128 (mtm-85) REVERT: B 658 MET cc_start: 0.5242 (tmm) cc_final: 0.4833 (tmm) REVERT: B 695 LEU cc_start: 0.7108 (mp) cc_final: 0.6620 (tt) REVERT: R 72 PHE cc_start: 0.8452 (m-10) cc_final: 0.7295 (m-10) REVERT: R 89 LEU cc_start: 0.9067 (tp) cc_final: 0.8378 (pt) REVERT: R 90 ASP cc_start: 0.9093 (p0) cc_final: 0.8664 (p0) outliers start: 17 outliers final: 12 residues processed: 263 average time/residue: 0.1000 time to fit residues: 38.2918 Evaluate side-chains 261 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 247 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 84 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 124 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 72 optimal weight: 30.0000 chunk 110 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 40.0000 chunk 81 optimal weight: 20.0000 chunk 112 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 HIS ** R 80 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 = 0.3601 r_free = 0.3601 target = 0.065978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.042524 restraints weight = 67463.373| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 3.25 r_work: 0.2657 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14974 Z= 0.258 Angle : 0.721 10.855 21501 Z= 0.397 Chirality : 0.045 0.228 2449 Planarity : 0.005 0.039 1707 Dihedral : 30.135 173.345 4349 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.85 % Allowed : 20.45 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.26 (0.27), residues: 1013 helix: 1.75 (0.20), residues: 647 sheet: -1.07 (0.80), residues: 48 loop : -0.74 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 99 TYR 0.032 0.002 TYR G 57 PHE 0.023 0.002 PHE R 13 TRP 0.073 0.005 TRP R 149 HIS 0.024 0.002 HIS R 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.26 (14957) covalent geometry : angle 0.71435 / 0.40 (21483) hydrogen bonds : bond 0.05564 / 3.73 ( 842) hydrogen bonds : angle 3.72385 / 2.73 ( 2144) metal coordination : bond 0.01891 / 1.04 ( 16) metal coordination : angle 3.46607 / 2.23 ( 18) Misc. bond : bond 0.00074 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8781 (mm-30) REVERT: D 43 LYS cc_start: 0.9716 (OUTLIER) cc_final: 0.9502 (mttp) REVERT: D 76 GLU cc_start: 0.9140 (tp30) cc_final: 0.8808 (tp30) REVERT: D 93 GLU cc_start: 0.9093 (mp0) cc_final: 0.8731 (mp0) REVERT: E 77 ASP cc_start: 0.9284 (m-30) cc_final: 0.9072 (p0) REVERT: F 84 MET cc_start: 0.9263 (mmm) cc_final: 0.9001 (tpp) REVERT: F 88 TYR cc_start: 0.9299 (m-10) cc_final: 0.8948 (m-10) REVERT: G 25 PHE cc_start: 0.8886 (m-80) cc_final: 0.8663 (m-80) REVERT: G 56 GLU cc_start: 0.9391 (tt0) cc_final: 0.9009 (tt0) REVERT: G 73 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8599 (t0) REVERT: G 90 ASP cc_start: 0.8743 (t0) cc_final: 0.8236 (t0) REVERT: H 42 TYR cc_start: 0.8955 (t80) cc_final: 0.8705 (t80) REVERT: H 44 VAL cc_start: 0.9796 (t) cc_final: 0.9567 (p) REVERT: H 46 LYS cc_start: 0.9257 (mmmt) cc_final: 0.9020 (mmmt) REVERT: H 68 ASP cc_start: 0.9427 (t0) cc_final: 0.9091 (t0) REVERT: H 79 ARG cc_start: 0.9293 (ttm-80) cc_final: 0.9037 (ttm110) REVERT: H 89 ILE cc_start: 0.9618 (mt) cc_final: 0.9411 (mp) REVERT: H 93 GLU cc_start: 0.9098 (mp0) cc_final: 0.8641 (mp0) REVERT: A 669 GLU cc_start: 0.8312 (pp20) cc_final: 0.7651 (tm-30) REVERT: A 673 LYS cc_start: 0.8759 (pttt) cc_final: 0.8486 (pttp) REVERT: A 680 MET cc_start: 0.8330 (ttm) cc_final: 0.8067 (ttm) REVERT: A 681 ARG cc_start: 0.8440 (mtm-85) cc_final: 0.8208 (mtm-85) REVERT: B 658 MET cc_start: 0.5372 (tmm) cc_final: 0.4969 (tmm) REVERT: R 90 ASP cc_start: 0.9160 (p0) cc_final: 0.8954 (p0) outliers start: 24 outliers final: 17 residues processed: 250 average time/residue: 0.1042 time to fit residues: 37.5436 Evaluate side-chains 251 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 1 optimal weight: 0.7980 chunk 113 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 50.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN A 699 HIS ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.067117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.043882 restraints weight = 67651.381| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.29 r_work: 0.2705 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 14974 Z= 0.140 Angle : 0.665 12.343 21501 Z= 0.374 Chirality : 0.043 0.242 2449 Planarity : 0.004 0.037 1707 Dihedral : 29.983 171.831 4349 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.78 % Allowed : 22.47 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 1.41 (0.27), residues: 1013 helix: 1.87 (0.20), residues: 646 sheet: -0.74 (0.83), residues: 44 loop : -0.72 (0.34), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 99 TYR 0.036 0.002 TYR G 57 PHE 0.030 0.002 PHE R 13 TRP 0.049 0.004 TRP R 149 HIS 0.026 0.002 HIS R 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (14957) covalent geometry : angle 0.65887 / 0.37 (21483) hydrogen bonds : bond 0.04182 / 2.68 ( 842) hydrogen bonds : angle 3.45861 / 2.55 ( 2144) metal coordination : bond 0.01167 / 0.64 ( 16) metal coordination : angle 3.06335 / 1.91 ( 18) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 250 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 LYS cc_start: 0.9662 (OUTLIER) cc_final: 0.9431 (mttp) REVERT: D 93 GLU cc_start: 0.9056 (mp0) cc_final: 0.8661 (mp0) REVERT: D 116 LYS cc_start: 0.9403 (ttpp) cc_final: 0.9148 (tmtt) REVERT: E 77 ASP cc_start: 0.9285 (m-30) cc_final: 0.9071 (p0) REVERT: F 84 MET cc_start: 0.9105 (mmm) cc_final: 0.8880 (tpp) REVERT: F 88 TYR cc_start: 0.9276 (m-10) cc_final: 0.8944 (m-10) REVERT: G 25 PHE cc_start: 0.8719 (m-80) cc_final: 0.8363 (m-80) REVERT: G 39 TYR cc_start: 0.9460 (m-80) cc_final: 0.8722 (m-80) REVERT: G 56 GLU cc_start: 0.9371 (tt0) cc_final: 0.9000 (tt0) REVERT: G 73 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8547 (t0) REVERT: G 90 ASP cc_start: 0.8632 (t0) cc_final: 0.8089 (t0) REVERT: H 42 TYR cc_start: 0.8887 (t80) cc_final: 0.8652 (t80) REVERT: H 46 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8974 (mmmt) REVERT: H 68 ASP cc_start: 0.9401 (t0) cc_final: 0.9080 (t0) REVERT: H 79 ARG cc_start: 0.9263 (ttm-80) cc_final: 0.9030 (ttm110) REVERT: H 93 GLU cc_start: 0.9074 (mp0) cc_final: 0.8649 (mp0) REVERT: H 105 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8597 (mm-30) REVERT: A 669 GLU cc_start: 0.8275 (pp20) cc_final: 0.7590 (tm-30) REVERT: A 673 LYS cc_start: 0.8767 (pttt) cc_final: 0.8558 (pttt) REVERT: A 680 MET cc_start: 0.8383 (ttm) cc_final: 0.8106 (ttm) REVERT: A 681 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8137 (mtm-85) REVERT: B 658 MET cc_start: 0.5002 (tmm) cc_final: 0.4624 (tmm) REVERT: B 680 MET cc_start: 0.6939 (tpp) cc_final: 0.5338 (ptp) REVERT: R 76 MET cc_start: 0.6225 (ptp) cc_final: 0.4210 (pmm) REVERT: R 89 LEU cc_start: 0.9006 (tp) cc_final: 0.8329 (pt) REVERT: R 90 ASP cc_start: 0.9047 (p0) cc_final: 0.8652 (p0) REVERT: R 92 LEU cc_start: 0.9227 (tp) cc_final: 0.8980 (tp) outliers start: 15 outliers final: 13 residues processed: 260 average time/residue: 0.1052 time to fit residues: 39.4950 Evaluate side-chains 257 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 242 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain A residue 699 HIS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 84 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 91 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 88 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** 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 = 0.3613 r_free = 0.3613 target = 0.066211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.043460 restraints weight = 67336.623| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.26 r_work: 0.2683 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14974 Z= 0.208 Angle : 0.693 11.636 21501 Z= 0.385 Chirality : 0.043 0.230 2449 Planarity : 0.005 0.070 1707 Dihedral : 30.041 172.473 4349 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.78 % Allowed : 22.71 % Favored : 75.51 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.50 % 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: 1.42 (0.27), residues: 1013 helix: 1.87 (0.20), residues: 646 sheet: -0.69 (0.85), residues: 44 loop : -0.72 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 99 TYR 0.035 0.002 TYR G 57 PHE 0.033 0.002 PHE R 13 TRP 0.044 0.004 TRP R 149 HIS 0.025 0.002 HIS R 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.21 (14957) covalent geometry : angle 0.68694 / 0.38 (21483) hydrogen bonds : bond 0.04611 / 3.03 ( 842) hydrogen bonds : angle 3.57676 / 2.64 ( 2144) metal coordination : bond 0.01469 / 0.81 ( 16) metal coordination : angle 3.12686 / 1.99 ( 18) Misc. bond : bond 0.00040 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2026 Ramachandran restraints generated. 1013 Oldfield, 0 Emsley, 1013 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 238 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 LYS cc_start: 0.9692 (OUTLIER) cc_final: 0.9453 (mttp) REVERT: D 93 GLU cc_start: 0.9100 (mp0) cc_final: 0.8704 (mp0) REVERT: F 84 MET cc_start: 0.9209 (mmm) cc_final: 0.8981 (tpp) REVERT: F 88 TYR cc_start: 0.9298 (m-10) cc_final: 0.8927 (m-10) REVERT: F 92 ARG cc_start: 0.9099 (tpt-90) cc_final: 0.8801 (ttt90) REVERT: G 25 PHE cc_start: 0.8957 (m-80) cc_final: 0.8591 (m-80) REVERT: G 39 TYR cc_start: 0.9495 (m-80) cc_final: 0.8920 (m-80) REVERT: G 56 GLU cc_start: 0.9369 (tt0) cc_final: 0.9005 (tt0) REVERT: G 73 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8585 (t0) REVERT: G 90 ASP cc_start: 0.8639 (t0) cc_final: 0.8124 (t0) REVERT: G 91 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8659 (tm-30) REVERT: H 42 TYR cc_start: 0.8920 (t80) cc_final: 0.8669 (t80) REVERT: H 46 LYS cc_start: 0.9224 (mmmt) cc_final: 0.9020 (mmmt) REVERT: H 68 ASP cc_start: 0.9451 (t0) cc_final: 0.9128 (t0) REVERT: H 79 ARG cc_start: 0.9330 (ttm-80) cc_final: 0.9085 (ttm110) REVERT: H 93 GLU cc_start: 0.9101 (mp0) cc_final: 0.8628 (mp0) REVERT: A 669 GLU cc_start: 0.8305 (pp20) cc_final: 0.7647 (tm-30) REVERT: A 673 LYS cc_start: 0.8758 (pttt) cc_final: 0.8476 (pttp) REVERT: A 680 MET cc_start: 0.8409 (ttm) cc_final: 0.8128 (ttm) REVERT: A 681 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8236 (mtm-85) REVERT: B 680 MET cc_start: 0.7030 (tpp) cc_final: 0.5400 (ptp) REVERT: R 76 MET cc_start: 0.6089 (ptp) cc_final: 0.4086 (pmm) REVERT: R 90 ASP cc_start: 0.9054 (p0) cc_final: 0.8844 (p0) outliers start: 15 outliers final: 12 residues processed: 246 average time/residue: 0.1063 time to fit residues: 37.4967 Evaluate side-chains 252 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 73 ASN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 7.9990 chunk 114 optimal weight: 0.1980 chunk 103 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 chunk 23 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN A 699 HIS ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.066779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.044160 restraints weight = 67420.664| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.27 r_work: 0.2708 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14974 Z= 0.149 Angle : 0.676 12.272 21501 Z= 0.378 Chirality : 0.043 0.238 2449 Planarity : 0.005 0.061 1707 Dihedral : 29.999 171.924 4349 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.90 % Allowed : 23.07 % Favored : 75.03 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.50 % 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: 1.43 (0.27), residues: 1013 helix: 1.89 (0.20), residues: 645 sheet: -0.55 (0.84), residues: 44 loop : -0.74 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.032 0.002 TYR G 57 PHE 0.031 0.002 PHE R 13 TRP 0.043 0.004 TRP R 149 HIS 0.027 0.002 HIS R 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (14957) covalent geometry : angle 0.67074 / 0.38 (21483) hydrogen bonds : bond 0.04256 / 2.75 ( 842) hydrogen bonds : angle 3.46874 / 2.57 ( 2144) metal coordination : bond 0.01180 / 0.66 ( 16) metal coordination : angle 3.03499 / 1.97 ( 18) Misc. bond : bond 0.00019 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3051.34 seconds wall clock time: 52 minutes 45.18 seconds (3165.18 seconds total)