Starting phenix.real_space_refine on Sat Aug 23 17:50:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ieg_35381/08_2025/8ieg_35381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ieg_35381/08_2025/8ieg_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_35381/08_2025/8ieg_35381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ieg_35381/08_2025/8ieg_35381.map" model { file = "/net/cci-nas-00/data/ceres_data/8ieg_35381/08_2025/8ieg_35381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ieg_35381/08_2025/8ieg_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-2.0-5787/lib/python3.9/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: 3.20, per 1000 atoms: 0.23 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: 1.23 Conformation dependent library (CDL) restraints added in 491.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 2.21 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: 2.80 Time building geometry restraints manager: 1.63 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' DT I -59 " pdb=" O3' DT I -59 " ideal model delta sigma weight residual 1.422 1.464 -0.042 3.00e-02 1.11e+03 1.94e+00 bond pdb=" CD GLU K 97 " pdb=" OE1 GLU K 97 " ideal model delta sigma weight residual 1.249 1.223 0.026 1.90e-02 2.77e+03 1.91e+00 bond pdb=" CG GLU K 97 " pdb=" CD GLU K 97 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.87e+00 bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.465 0.048 3.90e-02 6.57e+02 1.49e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.46e+00 ... (remaining 14952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 20862 1.60 - 3.20: 586 3.20 - 4.80: 25 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=" N GLU K 97 " pdb=" CA GLU K 97 " pdb=" CB GLU K 97 " ideal model delta sigma weight residual 110.12 115.83 -5.71 1.47e+00 4.63e-01 1.51e+01 angle pdb=" N MET B 680 " pdb=" CA MET B 680 " pdb=" C MET B 680 " ideal model delta sigma weight residual 110.68 105.93 4.75 1.39e+00 5.18e-01 1.17e+01 angle pdb=" C THR E 80 " pdb=" N ASP E 81 " pdb=" CA ASP E 81 " ideal model delta sigma weight residual 122.46 126.81 -4.35 1.41e+00 5.03e-01 9.53e+00 ... (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 - 0.033: 1694 0.033 - 0.067: 595 0.067 - 0.100: 110 0.100 - 0.133: 44 0.133 - 0.166: 6 Chirality restraints: 2449 Sorted by residual: 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 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.070 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.455 14974 Z= 0.408 Angle : 0.614 8.875 21501 Z= 0.386 Chirality : 0.036 0.166 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 aren 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 covalent geometry : bond 0.00352 (14957) covalent geometry : angle 0.60373 (21483) hydrogen bonds : bond 0.13474 ( 842) hydrogen bonds : angle 4.76814 ( 2144) metal coordination : bond 0.01304 ( 16) metal coordination : angle 3.96135 ( 18) Misc. bond : bond 0.45518 ( 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 : 0.419 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: 0.1469 time to fit residues: 78.7309 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 : 0.408 ------------------------------------------------------------------------------- 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: 8.9990 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... Flipped N/Q/H residues before XYZ refinement: ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 49 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS 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 = 0.3676 r_free = 0.3676 target = 0.069645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046315 restraints weight = 66194.836| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 3.35 r_work: 0.2758 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14974 Z= 0.157 Angle : 0.595 6.777 21501 Z= 0.345 Chirality : 0.035 0.148 2449 Planarity : 0.004 0.045 1707 Dihedral : 29.012 170.318 4362 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.26 % Allowed : 14.63 % Favored : 83.12 % 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 aren not related in a simple way. whole: 1.21 (0.27), residues: 1013 helix: 1.65 (0.20), residues: 649 sheet: -1.51 (0.73), residues: 50 loop : -0.52 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 35 TYR 0.015 0.001 TYR D 40 PHE 0.020 0.002 PHE R 72 TRP 0.042 0.003 TRP R 149 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00345 (14957) covalent geometry : angle 0.58477 (21483) hydrogen bonds : bond 0.04015 ( 842) hydrogen bonds : angle 3.35231 ( 2144) metal coordination : bond 0.01135 ( 16) metal coordination : angle 3.89985 ( 18) Misc. bond : bond 0.00054 ( 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 306 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 287 time to evaluate : 0.415 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: K 59 GLU cc_start: 0.8918 (pm20) cc_final: 0.8652 (pm20) REVERT: K 105 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8850 (mt-10) REVERT: L 84 MET cc_start: 0.9444 (mmm) cc_final: 0.9224 (mmm) REVERT: C 39 TYR cc_start: 0.8705 (m-80) cc_final: 0.8426 (m-80) REVERT: C 91 GLU cc_start: 0.8242 (pm20) cc_final: 0.7854 (pm20) REVERT: C 92 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8696 (mm-30) REVERT: D 71 GLU cc_start: 0.9297 (tp30) cc_final: 0.9084 (tp30) REVERT: D 93 GLU cc_start: 0.8991 (mp0) cc_final: 0.8646 (mp0) REVERT: E 77 ASP cc_start: 0.9331 (m-30) cc_final: 0.8911 (p0) REVERT: E 79 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7702 (tttt) REVERT: F 64 ASN cc_start: 0.9472 (m110) cc_final: 0.9235 (m110) REVERT: F 74 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8522 (mt-10) REVERT: F 88 TYR cc_start: 0.9139 (m-10) cc_final: 0.8937 (m-10) REVERT: G 25 PHE cc_start: 0.9161 (m-80) cc_final: 0.8926 (m-80) REVERT: G 39 TYR cc_start: 0.9274 (m-80) cc_final: 0.8735 (m-80) REVERT: G 56 GLU cc_start: 0.9293 (tt0) cc_final: 0.9003 (tt0) REVERT: G 90 ASP cc_start: 0.8586 (t0) cc_final: 0.8192 (t0) REVERT: G 92 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8525 (mt-10) REVERT: H 33 ARG cc_start: 0.5394 (mtp85) cc_final: 0.4293 (ttm170) REVERT: H 83 TYR cc_start: 0.8092 (m-10) cc_final: 0.7222 (m-80) REVERT: H 93 GLU cc_start: 0.8891 (mp0) cc_final: 0.8665 (mp0) REVERT: H 101 LEU cc_start: 0.9527 (mm) cc_final: 0.9314 (mt) REVERT: A 669 GLU cc_start: 0.8080 (pp20) cc_final: 0.7349 (tm-30) REVERT: A 673 LYS cc_start: 0.8869 (pttt) cc_final: 0.8655 (pttp) REVERT: A 674 GLU cc_start: 0.8821 (pp20) cc_final: 0.8563 (pt0) REVERT: A 680 MET cc_start: 0.8536 (ttm) cc_final: 0.8255 (ttm) REVERT: A 681 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7469 (mtm-85) REVERT: R 8 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.8073 (tpt-90) REVERT: R 36 TRP cc_start: 0.5859 (m100) cc_final: 0.5333 (m100) REVERT: R 52 THR cc_start: 0.7840 (p) cc_final: 0.7566 (p) REVERT: R 72 PHE cc_start: 0.8751 (m-80) cc_final: 0.8073 (m-80) REVERT: R 89 LEU cc_start: 0.9027 (tp) cc_final: 0.8826 (tp) REVERT: R 110 GLN cc_start: 0.2580 (OUTLIER) cc_final: 0.2140 (tp40) outliers start: 19 outliers final: 10 residues processed: 297 average time/residue: 0.1223 time to fit residues: 50.9392 Evaluate side-chains 268 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 255 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 8 ARG Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 101 ASP 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: 8.9990 chunk 87 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 71 optimal weight: 10.0000 chunk 47 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 113 HIS C 73 ASN E 68 GLN G 73 ASN G 104 GLN ** 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 = 0.3625 r_free = 0.3625 target = 0.066869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.043419 restraints weight = 66773.480| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.34 r_work: 0.2682 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14974 Z= 0.221 Angle : 0.610 8.539 21501 Z= 0.350 Chirality : 0.037 0.143 2449 Planarity : 0.004 0.035 1707 Dihedral : 29.518 171.980 4358 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.80 % Allowed : 14.63 % Favored : 81.57 % 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 aren not related in a simple way. whole: 1.48 (0.27), residues: 1013 helix: 1.83 (0.20), residues: 650 sheet: -0.89 (0.79), residues: 48 loop : -0.47 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 92 TYR 0.018 0.002 TYR R 137 PHE 0.028 0.002 PHE R 13 TRP 0.019 0.003 TRP R 149 HIS 0.007 0.001 HIS L 75 Details of bonding type rmsd covalent geometry : bond 0.00501 (14957) covalent geometry : angle 0.59976 (21483) hydrogen bonds : bond 0.04355 ( 842) hydrogen bonds : angle 3.41095 ( 2144) metal coordination : bond 0.01620 ( 16) metal coordination : angle 3.94940 ( 18) Misc. bond : bond 0.00094 ( 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 293 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 261 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 59 GLU cc_start: 0.9035 (pm20) cc_final: 0.8658 (pm20) REVERT: K 105 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8953 (mt-10) REVERT: L 44 LYS cc_start: 0.9326 (mtpt) cc_final: 0.9074 (mtpt) REVERT: C 92 GLU cc_start: 0.9162 (mm-30) cc_final: 0.8941 (mm-30) REVERT: D 93 GLU cc_start: 0.9045 (mp0) cc_final: 0.8597 (mp0) REVERT: E 77 ASP cc_start: 0.9251 (m-30) cc_final: 0.8937 (p0) REVERT: E 79 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.6873 (tttt) REVERT: F 88 TYR cc_start: 0.9195 (m-10) cc_final: 0.8959 (m-80) REVERT: G 56 GLU cc_start: 0.9305 (tt0) cc_final: 0.9039 (tt0) REVERT: G 90 ASP cc_start: 0.8723 (t0) cc_final: 0.8342 (t0) REVERT: G 92 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8589 (mt-10) REVERT: H 83 TYR cc_start: 0.8173 (m-10) cc_final: 0.6986 (m-10) REVERT: H 89 ILE cc_start: 0.9643 (mt) cc_final: 0.9402 (mp) REVERT: H 93 GLU cc_start: 0.9087 (mp0) cc_final: 0.8661 (mp0) REVERT: H 101 LEU cc_start: 0.9467 (mm) cc_final: 0.9139 (mm) REVERT: A 669 GLU cc_start: 0.8227 (pp20) cc_final: 0.7548 (tm-30) REVERT: A 680 MET cc_start: 0.8406 (ttm) cc_final: 0.8046 (ttm) REVERT: B 680 MET cc_start: 0.6927 (tpt) cc_final: 0.5974 (ptp) outliers start: 32 outliers final: 13 residues processed: 276 average time/residue: 0.1146 time to fit residues: 45.3243 Evaluate side-chains 254 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 240 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.0470 overall best weight: 2.1484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3617 r_free = 0.3617 target = 0.066474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.043636 restraints weight = 67130.667| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 3.29 r_work: 0.2686 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14974 Z= 0.198 Angle : 0.608 7.802 21501 Z= 0.349 Chirality : 0.037 0.180 2449 Planarity : 0.004 0.033 1707 Dihedral : 29.484 171.386 4349 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.85 % Allowed : 18.43 % Favored : 78.72 % 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 aren not related in a simple way. whole: 1.58 (0.27), residues: 1013 helix: 1.94 (0.20), residues: 648 sheet: -0.54 (0.81), residues: 47 loop : -0.53 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.016 0.001 TYR R 137 PHE 0.027 0.002 PHE R 72 TRP 0.026 0.003 TRP R 36 HIS 0.012 0.001 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00446 (14957) covalent geometry : angle 0.60010 (21483) hydrogen bonds : bond 0.04040 ( 842) hydrogen bonds : angle 3.35790 ( 2144) metal coordination : bond 0.01333 ( 16) metal coordination : angle 3.36573 ( 18) Misc. bond : bond 0.00056 ( 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 281 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 257 time to evaluate : 0.501 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 59 GLU cc_start: 0.9015 (pm20) cc_final: 0.8594 (pm20) REVERT: C 39 TYR cc_start: 0.8934 (m-80) cc_final: 0.8664 (m-80) REVERT: D 43 LYS cc_start: 0.9666 (OUTLIER) cc_final: 0.9434 (mttp) REVERT: D 93 GLU cc_start: 0.9031 (mp0) cc_final: 0.8667 (mp0) REVERT: E 77 ASP cc_start: 0.9207 (m-30) cc_final: 0.8971 (p0) REVERT: E 79 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7084 (mtpt) REVERT: F 88 TYR cc_start: 0.9245 (m-10) cc_final: 0.8756 (m-80) REVERT: G 39 TYR cc_start: 0.9441 (m-80) cc_final: 0.8877 (m-80) REVERT: G 56 GLU cc_start: 0.9308 (tt0) cc_final: 0.8987 (tt0) REVERT: G 90 ASP cc_start: 0.8695 (t0) cc_final: 0.8284 (t0) REVERT: H 33 ARG cc_start: 0.5451 (mtp85) cc_final: 0.5186 (mtt90) REVERT: H 83 TYR cc_start: 0.8147 (m-10) cc_final: 0.6976 (m-10) REVERT: H 93 GLU cc_start: 0.9084 (mp0) cc_final: 0.8674 (mp0) REVERT: H 101 LEU cc_start: 0.9432 (mm) cc_final: 0.9119 (mm) REVERT: A 661 LYS cc_start: 0.8444 (ttmt) cc_final: 0.7864 (mttm) REVERT: A 669 GLU cc_start: 0.8322 (pp20) cc_final: 0.7614 (tm-30) REVERT: A 680 MET cc_start: 0.8367 (ttm) cc_final: 0.8103 (ttm) REVERT: B 695 LEU cc_start: 0.7194 (tt) cc_final: 0.6732 (mt) REVERT: R 39 MET cc_start: 0.8180 (tpp) cc_final: 0.7935 (tpp) outliers start: 24 outliers final: 19 residues processed: 268 average time/residue: 0.1375 time to fit residues: 51.9167 Evaluate side-chains 265 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 124 ILE 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 106 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 130 PHE 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: 4.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 20.0000 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.066802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.043008 restraints weight = 68844.427| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.42 r_work: 0.2683 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14974 Z= 0.188 Angle : 0.600 9.264 21501 Z= 0.345 Chirality : 0.036 0.157 2449 Planarity : 0.004 0.031 1707 Dihedral : 29.494 170.294 4349 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.57 % Allowed : 19.26 % Favored : 77.17 % 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 aren not related in a simple way. whole: 1.74 (0.27), residues: 1013 helix: 2.07 (0.20), residues: 648 sheet: -0.37 (0.82), residues: 47 loop : -0.52 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.014 0.001 TYR D 121 PHE 0.019 0.002 PHE R 13 TRP 0.027 0.003 TRP R 36 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00423 (14957) covalent geometry : angle 0.59327 (21483) hydrogen bonds : bond 0.03992 ( 842) hydrogen bonds : angle 3.32132 ( 2144) metal coordination : bond 0.01391 ( 16) metal coordination : angle 3.05591 ( 18) Misc. bond : bond 0.00066 ( 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 282 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 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: symmetry clash REVERT: K 59 GLU cc_start: 0.9011 (pm20) cc_final: 0.8416 (pm20) REVERT: D 43 LYS cc_start: 0.9703 (OUTLIER) cc_final: 0.9485 (mttp) REVERT: D 93 GLU cc_start: 0.9097 (mp0) cc_final: 0.8632 (mp0) REVERT: E 77 ASP cc_start: 0.9239 (m-30) cc_final: 0.9032 (p0) REVERT: E 79 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7483 (mttt) REVERT: F 84 MET cc_start: 0.9165 (mmm) cc_final: 0.8787 (tpp) REVERT: F 85 ASP cc_start: 0.8915 (m-30) cc_final: 0.8514 (m-30) REVERT: G 39 TYR cc_start: 0.9483 (m-80) cc_final: 0.8859 (m-80) REVERT: G 56 GLU cc_start: 0.9336 (tt0) cc_final: 0.9020 (tt0) REVERT: G 90 ASP cc_start: 0.8636 (t0) cc_final: 0.8113 (t0) REVERT: H 34 LYS cc_start: 0.6833 (tttp) cc_final: 0.6625 (tptt) REVERT: H 46 LYS cc_start: 0.9303 (mmmt) cc_final: 0.9082 (mmmt) REVERT: H 93 GLU cc_start: 0.9160 (mp0) cc_final: 0.8660 (mp0) REVERT: H 101 LEU cc_start: 0.9371 (mm) cc_final: 0.9080 (mm) REVERT: A 661 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7968 (mttm) REVERT: A 669 GLU cc_start: 0.8520 (pp20) cc_final: 0.7756 (tm-30) REVERT: A 673 LYS cc_start: 0.8768 (pttm) cc_final: 0.8509 (pttm) REVERT: A 674 GLU cc_start: 0.8944 (pp20) cc_final: 0.8583 (pt0) REVERT: A 680 MET cc_start: 0.8228 (ttm) cc_final: 0.7971 (ttm) REVERT: B 680 MET cc_start: 0.7043 (tpt) cc_final: 0.5820 (ptp) REVERT: B 695 LEU cc_start: 0.6903 (tt) cc_final: 0.6443 (mt) outliers start: 30 outliers final: 21 residues processed: 268 average time/residue: 0.1402 time to fit residues: 52.8706 Evaluate side-chains 269 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 68 GLN Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 124 ILE 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 H residue 111 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 130 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 38 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 116 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 119 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN E 85 GLN G 73 ASN ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.064855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.041121 restraints weight = 67161.160| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.39 r_work: 0.2624 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 14974 Z= 0.291 Angle : 0.677 9.792 21501 Z= 0.382 Chirality : 0.040 0.157 2449 Planarity : 0.005 0.047 1707 Dihedral : 30.001 169.938 4349 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.92 % Allowed : 19.14 % Favored : 76.93 % 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 aren not related in a simple way. whole: 1.41 (0.27), residues: 1013 helix: 1.82 (0.20), residues: 648 sheet: -0.32 (0.84), residues: 47 loop : -0.70 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 69 TYR 0.022 0.002 TYR C 39 PHE 0.021 0.002 PHE R 13 TRP 0.028 0.003 TRP R 36 HIS 0.016 0.002 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00659 (14957) covalent geometry : angle 0.66630 (21483) hydrogen bonds : bond 0.05152 ( 842) hydrogen bonds : angle 3.68778 ( 2144) metal coordination : bond 0.01940 ( 16) metal coordination : angle 4.13979 ( 18) Misc. bond : bond 0.00113 ( 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 272 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 LYS cc_start: 0.9732 (OUTLIER) cc_final: 0.9508 (mttp) REVERT: D 76 GLU cc_start: 0.9163 (tp30) cc_final: 0.8817 (tp30) REVERT: D 93 GLU cc_start: 0.9135 (mp0) cc_final: 0.8654 (mp0) REVERT: G 39 TYR cc_start: 0.9527 (m-80) cc_final: 0.9021 (m-80) REVERT: G 56 GLU cc_start: 0.9297 (tt0) cc_final: 0.9002 (tt0) REVERT: G 90 ASP cc_start: 0.8744 (t0) cc_final: 0.8253 (t0) REVERT: H 34 LYS cc_start: 0.6949 (tttp) cc_final: 0.6664 (tptt) REVERT: H 46 LYS cc_start: 0.9293 (mmmt) cc_final: 0.9092 (mmmt) REVERT: H 93 GLU cc_start: 0.9180 (mp0) cc_final: 0.8664 (mp0) REVERT: A 669 GLU cc_start: 0.8601 (pp20) cc_final: 0.7898 (tm-30) REVERT: A 674 GLU cc_start: 0.9091 (pp20) cc_final: 0.8724 (pt0) REVERT: A 680 MET cc_start: 0.8351 (ttm) cc_final: 0.8031 (ttm) REVERT: A 682 LYS cc_start: 0.9251 (mmmt) cc_final: 0.8935 (mmmt) REVERT: B 695 LEU cc_start: 0.6701 (tt) cc_final: 0.6276 (mt) outliers start: 33 outliers final: 27 residues processed: 259 average time/residue: 0.1410 time to fit residues: 51.4138 Evaluate side-chains 258 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 230 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 102 ILE Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 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 H residue 90 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 130 PHE Chi-restraints excluded: chain R residue 133 HIS 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: 9.9990 chunk 69 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 chunk 104 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 HIS R 133 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.066737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.043762 restraints weight = 68490.928| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.26 r_work: 0.2703 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14974 Z= 0.151 Angle : 0.612 11.190 21501 Z= 0.348 Chirality : 0.035 0.155 2449 Planarity : 0.004 0.052 1707 Dihedral : 29.454 168.007 4349 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.26 % Allowed : 22.24 % Favored : 75.51 % 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 aren not related in a simple way. whole: 1.65 (0.27), residues: 1013 helix: 2.03 (0.20), residues: 648 sheet: -0.29 (0.82), residues: 47 loop : -0.64 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.015 0.001 TYR G 57 PHE 0.013 0.002 PHE R 130 TRP 0.019 0.002 TRP R 36 HIS 0.015 0.001 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00331 (14957) covalent geometry : angle 0.60717 (21483) hydrogen bonds : bond 0.03710 ( 842) hydrogen bonds : angle 3.31337 ( 2144) metal coordination : bond 0.00915 ( 16) metal coordination : angle 2.61933 ( 18) Misc. bond : bond 0.00001 ( 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 280 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 261 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 59 GLU cc_start: 0.8999 (pm20) cc_final: 0.8515 (pm20) REVERT: C 38 ASN cc_start: 0.9137 (m-40) cc_final: 0.8935 (t0) REVERT: D 76 GLU cc_start: 0.9121 (tp30) cc_final: 0.8783 (tp30) REVERT: D 89 ILE cc_start: 0.9694 (mt) cc_final: 0.9493 (mp) REVERT: D 93 GLU cc_start: 0.9048 (mp0) cc_final: 0.8608 (mp0) REVERT: E 79 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8276 (mttt) REVERT: E 90 MET cc_start: 0.9273 (mmm) cc_final: 0.8999 (mmm) REVERT: F 92 ARG cc_start: 0.8911 (ttt90) cc_final: 0.8676 (ttt-90) REVERT: G 39 TYR cc_start: 0.9454 (m-80) cc_final: 0.8875 (m-80) REVERT: G 56 GLU cc_start: 0.9277 (tt0) cc_final: 0.8981 (tt0) REVERT: G 90 ASP cc_start: 0.8624 (t0) cc_final: 0.8052 (t0) REVERT: G 92 GLU cc_start: 0.8550 (tt0) cc_final: 0.8293 (tt0) REVERT: H 46 LYS cc_start: 0.9348 (mmmt) cc_final: 0.9082 (mmmt) REVERT: H 89 ILE cc_start: 0.9598 (mt) cc_final: 0.9384 (mp) REVERT: H 93 GLU cc_start: 0.9129 (mp0) cc_final: 0.8667 (mp0) REVERT: A 669 GLU cc_start: 0.8628 (pp20) cc_final: 0.7776 (tm-30) REVERT: A 673 LYS cc_start: 0.8872 (pttm) cc_final: 0.8585 (pttm) REVERT: A 674 GLU cc_start: 0.9115 (pp20) cc_final: 0.8719 (pt0) REVERT: A 679 ARG cc_start: 0.9130 (mtp85) cc_final: 0.8889 (mtp85) REVERT: A 680 MET cc_start: 0.8585 (ttm) cc_final: 0.8159 (ttm) REVERT: A 681 ARG cc_start: 0.8662 (ptp90) cc_final: 0.8393 (ptp90) REVERT: A 682 LYS cc_start: 0.9287 (mmmt) cc_final: 0.9026 (mmmt) REVERT: B 680 MET cc_start: 0.7504 (tpp) cc_final: 0.6224 (ptp) REVERT: B 695 LEU cc_start: 0.6770 (tt) cc_final: 0.6426 (mt) outliers start: 19 outliers final: 16 residues processed: 271 average time/residue: 0.1391 time to fit residues: 53.4255 Evaluate side-chains 265 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 60 LEU 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 90 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 133 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 124 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 78 HIS ** 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 = 0.3558 r_free = 0.3558 target = 0.063667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.040311 restraints weight = 68747.286| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.37 r_work: 0.2600 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.074 14974 Z= 0.391 Angle : 0.761 11.889 21501 Z= 0.421 Chirality : 0.043 0.164 2449 Planarity : 0.005 0.063 1707 Dihedral : 30.161 169.221 4349 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.69 % Allowed : 21.88 % Favored : 74.44 % 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 aren not related in a simple way. whole: 1.09 (0.27), residues: 1013 helix: 1.57 (0.20), residues: 648 sheet: -0.19 (0.87), residues: 47 loop : -0.87 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 99 TYR 0.022 0.003 TYR C 39 PHE 0.036 0.003 PHE R 72 TRP 0.039 0.004 TRP R 149 HIS 0.023 0.002 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00880 (14957) covalent geometry : angle 0.74841 (21483) hydrogen bonds : bond 0.06043 ( 842) hydrogen bonds : angle 4.00443 ( 2144) metal coordination : bond 0.02270 ( 16) metal coordination : angle 4.81405 ( 18) Misc. bond : bond 0.00117 ( 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: 31 poor density : 230 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 31 ARG cc_start: 0.5733 (tpm170) cc_final: 0.5424 (tpt90) REVERT: D 76 GLU cc_start: 0.9183 (tp30) cc_final: 0.8867 (tp30) REVERT: D 93 GLU cc_start: 0.9175 (mp0) cc_final: 0.8725 (mp0) REVERT: G 39 TYR cc_start: 0.9558 (m-80) cc_final: 0.9013 (m-80) REVERT: G 56 GLU cc_start: 0.9329 (tt0) cc_final: 0.8979 (tt0) REVERT: G 90 ASP cc_start: 0.8800 (t0) cc_final: 0.8373 (t0) REVERT: H 34 LYS cc_start: 0.6603 (tptt) cc_final: 0.6015 (tppt) REVERT: H 46 LYS cc_start: 0.9279 (mmmt) cc_final: 0.9042 (mmmt) REVERT: H 93 GLU cc_start: 0.9185 (mp0) cc_final: 0.8657 (mp0) REVERT: A 669 GLU cc_start: 0.8734 (pp20) cc_final: 0.7991 (tm-30) REVERT: A 673 LYS cc_start: 0.8830 (pttm) cc_final: 0.8612 (pttm) REVERT: A 680 MET cc_start: 0.8353 (ttm) cc_final: 0.7772 (ttm) REVERT: A 681 ARG cc_start: 0.8464 (ptp90) cc_final: 0.8213 (ptp90) REVERT: B 680 MET cc_start: 0.7654 (tpp) cc_final: 0.6527 (ptp) REVERT: B 695 LEU cc_start: 0.6917 (tt) cc_final: 0.6409 (mt) outliers start: 31 outliers final: 23 residues processed: 248 average time/residue: 0.1425 time to fit residues: 49.9806 Evaluate side-chains 242 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 219 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain D residue 90 THR 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 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 H residue 90 THR Chi-restraints excluded: chain H residue 95 GLN Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 84 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 1 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.066186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.043769 restraints weight = 66438.091| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.34 r_work: 0.2703 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14974 Z= 0.159 Angle : 0.656 11.803 21501 Z= 0.365 Chirality : 0.036 0.152 2449 Planarity : 0.004 0.062 1707 Dihedral : 29.487 166.811 4349 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.50 % Allowed : 24.14 % Favored : 73.37 % 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 aren not related in a simple way. whole: 1.44 (0.27), residues: 1013 helix: 1.88 (0.21), residues: 648 sheet: -0.18 (0.84), residues: 47 loop : -0.79 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 99 TYR 0.019 0.002 TYR R 137 PHE 0.020 0.002 PHE R 13 TRP 0.042 0.003 TRP R 149 HIS 0.026 0.001 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00353 (14957) covalent geometry : angle 0.65075 (21483) hydrogen bonds : bond 0.03791 ( 842) hydrogen bonds : angle 3.45823 ( 2144) metal coordination : bond 0.01126 ( 16) metal coordination : angle 2.84903 ( 18) Misc. bond : bond 0.00018 ( 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 267 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 246 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 59 GLU cc_start: 0.9034 (pm20) cc_final: 0.8538 (pm20) REVERT: C 38 ASN cc_start: 0.9275 (t0) cc_final: 0.9018 (t0) REVERT: D 35 GLU cc_start: 0.7155 (pp20) cc_final: 0.6699 (pp20) REVERT: D 76 GLU cc_start: 0.9158 (tp30) cc_final: 0.8843 (tp30) REVERT: D 89 ILE cc_start: 0.9680 (mt) cc_final: 0.9468 (mp) REVERT: D 93 GLU cc_start: 0.9149 (mp0) cc_final: 0.8635 (mp0) REVERT: D 116 LYS cc_start: 0.9466 (ttpp) cc_final: 0.9213 (tmtt) REVERT: E 79 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7962 (tttt) REVERT: G 56 GLU cc_start: 0.9281 (tt0) cc_final: 0.8956 (tt0) REVERT: G 90 ASP cc_start: 0.8599 (t0) cc_final: 0.8032 (t0) REVERT: G 92 GLU cc_start: 0.8510 (tt0) cc_final: 0.8277 (tt0) REVERT: H 33 ARG cc_start: 0.4930 (ttt180) cc_final: 0.4456 (ttm170) REVERT: H 46 LYS cc_start: 0.9327 (mmmt) cc_final: 0.9055 (mmmt) REVERT: H 93 GLU cc_start: 0.9153 (mp0) cc_final: 0.8665 (mp0) REVERT: H 101 LEU cc_start: 0.9455 (mm) cc_final: 0.9224 (mt) REVERT: A 658 MET cc_start: 0.8016 (tpp) cc_final: 0.7731 (tpp) REVERT: A 669 GLU cc_start: 0.8604 (pp20) cc_final: 0.7745 (tm-30) REVERT: A 673 LYS cc_start: 0.8850 (pttm) cc_final: 0.8625 (pttm) REVERT: A 680 MET cc_start: 0.8546 (ttm) cc_final: 0.8036 (ttm) REVERT: B 680 MET cc_start: 0.7407 (tpp) cc_final: 0.6262 (ptp) REVERT: B 695 LEU cc_start: 0.6974 (tt) cc_final: 0.6528 (mt) REVERT: R 82 TYR cc_start: 0.8799 (m-10) cc_final: 0.8503 (m-80) REVERT: R 129 LEU cc_start: 0.5675 (tp) cc_final: 0.4705 (mt) outliers start: 21 outliers final: 15 residues processed: 257 average time/residue: 0.1395 time to fit residues: 51.0683 Evaluate side-chains 257 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 241 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain E residue 56 LYS 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 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 133 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.066380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.043239 restraints weight = 68057.146| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.43 r_work: 0.2692 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14974 Z= 0.171 Angle : 0.661 11.792 21501 Z= 0.368 Chirality : 0.036 0.152 2449 Planarity : 0.004 0.041 1707 Dihedral : 29.509 167.161 4349 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.38 % Allowed : 24.61 % Favored : 73.01 % 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 aren not related in a simple way. whole: 1.42 (0.27), residues: 1013 helix: 1.85 (0.20), residues: 648 sheet: -0.23 (0.83), residues: 47 loop : -0.75 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.025 0.002 TYR H 83 PHE 0.023 0.002 PHE R 13 TRP 0.038 0.003 TRP R 149 HIS 0.027 0.001 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00384 (14957) covalent geometry : angle 0.65641 (21483) hydrogen bonds : bond 0.03872 ( 842) hydrogen bonds : angle 3.47066 ( 2144) metal coordination : bond 0.01258 ( 16) metal coordination : angle 2.63356 ( 18) Misc. bond : bond 0.00020 ( 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 263 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 59 GLU cc_start: 0.9020 (pm20) cc_final: 0.8448 (pm20) REVERT: L 84 MET cc_start: 0.9515 (mmm) cc_final: 0.9002 (mmm) REVERT: C 38 ASN cc_start: 0.9243 (t0) cc_final: 0.9025 (t0) REVERT: D 35 GLU cc_start: 0.7129 (pp20) cc_final: 0.6718 (pp20) REVERT: D 76 GLU cc_start: 0.9163 (tp30) cc_final: 0.8846 (tp30) REVERT: D 89 ILE cc_start: 0.9679 (mt) cc_final: 0.9466 (mp) REVERT: D 93 GLU cc_start: 0.9148 (mp0) cc_final: 0.8638 (mp0) REVERT: D 116 LYS cc_start: 0.9463 (ttpp) cc_final: 0.9215 (tmtt) REVERT: E 79 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.7932 (tttt) REVERT: E 90 MET cc_start: 0.9333 (mmm) cc_final: 0.9077 (mmm) REVERT: G 56 GLU cc_start: 0.9370 (tt0) cc_final: 0.9059 (tt0) REVERT: G 90 ASP cc_start: 0.8677 (t0) cc_final: 0.8161 (t0) REVERT: H 33 ARG cc_start: 0.4957 (ttt180) cc_final: 0.4434 (ttm170) REVERT: H 46 LYS cc_start: 0.9349 (mmmt) cc_final: 0.9087 (mmmt) REVERT: H 101 LEU cc_start: 0.9493 (mm) cc_final: 0.9252 (mt) REVERT: A 658 MET cc_start: 0.7936 (tpp) cc_final: 0.7667 (tpp) REVERT: A 669 GLU cc_start: 0.8673 (pp20) cc_final: 0.7761 (tm-30) REVERT: A 673 LYS cc_start: 0.8844 (pttm) cc_final: 0.8572 (pttp) REVERT: A 680 MET cc_start: 0.8357 (ttm) cc_final: 0.7916 (ttm) REVERT: B 680 MET cc_start: 0.7504 (tpp) cc_final: 0.6414 (ptp) REVERT: B 695 LEU cc_start: 0.6675 (tt) cc_final: 0.6298 (mt) REVERT: R 76 MET cc_start: 0.7255 (pmm) cc_final: 0.4888 (ppp) REVERT: R 82 TYR cc_start: 0.8892 (m-10) cc_final: 0.8486 (m-80) REVERT: R 129 LEU cc_start: 0.5702 (tp) cc_final: 0.4786 (mt) outliers start: 20 outliers final: 17 residues processed: 253 average time/residue: 0.1328 time to fit residues: 48.1254 Evaluate side-chains 259 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 241 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 60 LEU 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 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 40 ILE Chi-restraints excluded: chain R residue 52 THR Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 84 ASN Chi-restraints excluded: chain R residue 133 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 0.0050 chunk 51 optimal weight: 4.9990 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.065336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.042140 restraints weight = 68273.298| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.41 r_work: 0.2661 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 14974 Z= 0.223 Angle : 0.682 11.590 21501 Z= 0.377 Chirality : 0.038 0.155 2449 Planarity : 0.004 0.040 1707 Dihedral : 29.627 167.208 4349 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.73 % Allowed : 24.26 % Favored : 73.01 % 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 aren not related in a simple way. whole: 1.38 (0.27), residues: 1013 helix: 1.83 (0.20), residues: 648 sheet: -0.31 (0.83), residues: 47 loop : -0.79 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 99 TYR 0.021 0.002 TYR H 83 PHE 0.026 0.002 PHE R 13 TRP 0.034 0.003 TRP R 149 HIS 0.023 0.001 HIS R 133 Details of bonding type rmsd covalent geometry : bond 0.00508 (14957) covalent geometry : angle 0.67715 (21483) hydrogen bonds : bond 0.04296 ( 842) hydrogen bonds : angle 3.58185 ( 2144) metal coordination : bond 0.01527 ( 16) metal coordination : angle 2.98126 ( 18) Misc. bond : bond 0.00041 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3759.84 seconds wall clock time: 64 minutes 59.84 seconds (3899.84 seconds total)