Starting phenix.real_space_refine on Thu Jul 31 19:11:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ieg_35381/07_2025/8ieg_35381.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ieg_35381/07_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_35381/07_2025/8ieg_35381.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ieg_35381/07_2025/8ieg_35381.map" model { file = "/net/cci-nas-00/data/ceres_data/8ieg_35381/07_2025/8ieg_35381.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ieg_35381/07_2025/8ieg_35381.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'ASP:plan': 5, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} 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: 8.11, per 1000 atoms: 0.58 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: 3.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 6.80 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: 5.28 Time building geometry restraints manager: 3.96 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 700 or resid 8 \ 01 through 802)) selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 31 through 119 or resid 121 through 124)) selection = (chain 'H' and (resid 31 through 119 or resid 121 through 124)) } ncs_group { reference = chain 'E' selection = (chain 'K' and resid 38 through 134) } ncs_group { reference = chain 'F' selection = (chain 'L' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.940 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.480 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP R 96 HIS 0.003 0.001 HIS C 82 PHE 0.016 0.002 PHE B 642 TYR 0.018 0.001 TYR D 40 ARG 0.007 0.001 ARG L 92 Details of bonding type rmsd hydrogen bonds : bond 0.13474 ( 842) hydrogen bonds : angle 4.76814 ( 2144) metal coordination : bond 0.01304 ( 16) metal coordination : angle 3.96135 ( 18) covalent geometry : bond 0.00352 (14957) covalent geometry : angle 0.60373 (21483) 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 : 1.150 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: 0.3413 time to fit residues: 181.8425 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 : 1.244 ------------------------------------------------------------------------------- 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 105 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 113 HIS 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 = 0.3644 r_free = 0.3644 target = 0.068177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.044611 restraints weight = 66183.176| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.35 r_work: 0.2713 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14974 Z= 0.197 Angle : 0.617 8.520 21501 Z= 0.355 Chirality : 0.037 0.147 2449 Planarity : 0.005 0.056 1707 Dihedral : 29.192 170.757 4362 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.38 % Allowed : 14.98 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.27), residues: 1013 helix: 1.64 (0.20), residues: 649 sheet: -1.62 (0.75), residues: 48 loop : -0.57 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP R 149 HIS 0.003 0.001 HIS C 31 PHE 0.022 0.002 PHE R 72 TYR 0.017 0.002 TYR R 100 ARG 0.008 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 842) hydrogen bonds : angle 3.41685 ( 2144) metal coordination : bond 0.01453 ( 16) metal coordination : angle 4.44098 ( 18) covalent geometry : bond 0.00442 (14957) covalent geometry : angle 0.60402 (21483) Misc. bond : bond 0.00152 ( 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 295 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 275 time to evaluate : 1.133 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: 0.9041 (pm20) cc_final: 0.8733 (pm20) REVERT: L 44 LYS cc_start: 0.9451 (tttt) cc_final: 0.9234 (mtpt) REVERT: C 39 TYR cc_start: 0.8803 (m-80) cc_final: 0.8491 (m-80) REVERT: C 91 GLU cc_start: 0.8354 (pm20) cc_final: 0.8006 (pm20) REVERT: C 92 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8750 (mm-30) REVERT: D 62 MET cc_start: 0.9478 (mmm) cc_final: 0.9247 (mmm) REVERT: D 71 GLU cc_start: 0.9344 (tp30) cc_final: 0.9102 (tp30) REVERT: D 90 THR cc_start: 0.9495 (p) cc_final: 0.9267 (p) REVERT: D 93 GLU cc_start: 0.9013 (mp0) cc_final: 0.8709 (mp0) REVERT: D 105 GLU cc_start: 0.7808 (tp30) cc_final: 0.7069 (tp30) REVERT: D 108 LYS cc_start: 0.9332 (ttmm) cc_final: 0.9086 (ttmm) REVERT: E 77 ASP cc_start: 0.9280 (m-30) cc_final: 0.8914 (p0) REVERT: E 79 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.7733 (tttt) REVERT: E 125 GLN cc_start: 0.9300 (mt0) cc_final: 0.9093 (mp10) REVERT: F 74 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8572 (mt-10) REVERT: F 88 TYR cc_start: 0.9172 (m-10) cc_final: 0.8924 (m-10) REVERT: G 39 TYR cc_start: 0.9370 (m-80) cc_final: 0.8825 (m-80) REVERT: G 56 GLU cc_start: 0.9276 (tt0) cc_final: 0.9009 (tt0) REVERT: G 90 ASP cc_start: 0.8595 (t0) cc_final: 0.8218 (t0) REVERT: G 92 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8514 (mt-10) REVERT: H 33 ARG cc_start: 0.5315 (mtp85) cc_final: 0.5096 (mtt90) REVERT: H 83 TYR cc_start: 0.8197 (m-10) cc_final: 0.7323 (m-80) REVERT: H 93 GLU cc_start: 0.8949 (mp0) cc_final: 0.8615 (mp0) REVERT: A 669 GLU cc_start: 0.8145 (pp20) cc_final: 0.7447 (tm-30) REVERT: A 680 MET cc_start: 0.8492 (ttm) cc_final: 0.8189 (ttm) REVERT: A 681 ARG cc_start: 0.8052 (mtm-85) cc_final: 0.7508 (mtm-85) REVERT: R 8 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8087 (tpt-90) REVERT: R 52 THR cc_start: 0.7977 (p) cc_final: 0.7732 (p) REVERT: R 110 GLN cc_start: 0.2408 (OUTLIER) cc_final: 0.2027 (tp40) outliers start: 20 outliers final: 11 residues processed: 286 average time/residue: 0.2844 time to fit residues: 113.7960 Evaluate side-chains 266 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER 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 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 53 PHE 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 14 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 117 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN G 73 ASN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.067861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.044368 restraints weight = 67969.210| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 3.39 r_work: 0.2713 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3180 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= 0.173 Angle : 0.589 7.904 21501 Z= 0.339 Chirality : 0.035 0.140 2449 Planarity : 0.004 0.035 1707 Dihedral : 29.314 171.431 4358 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.62 % Allowed : 16.17 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.27), residues: 1013 helix: 1.93 (0.21), residues: 648 sheet: -1.13 (0.76), residues: 48 loop : -0.45 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP R 149 HIS 0.011 0.001 HIS R 133 PHE 0.026 0.002 PHE R 13 TYR 0.020 0.001 TYR R 137 ARG 0.004 0.000 ARG H 86 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 842) hydrogen bonds : angle 3.25615 ( 2144) metal coordination : bond 0.01214 ( 16) metal coordination : angle 3.70008 ( 18) covalent geometry : bond 0.00383 (14957) covalent geometry : angle 0.57967 (21483) Misc. bond : bond 0.00083 ( 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 292 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 270 time to evaluate : 1.218 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: 0.9029 (pm20) cc_final: 0.8675 (pm20) REVERT: L 74 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8912 (tm-30) REVERT: C 92 GLU cc_start: 0.9116 (mm-30) cc_final: 0.8902 (mm-30) REVERT: D 90 THR cc_start: 0.9508 (p) cc_final: 0.9253 (p) REVERT: D 92 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8621 (ttt180) REVERT: D 93 GLU cc_start: 0.9061 (mp0) cc_final: 0.8649 (mp0) REVERT: E 77 ASP cc_start: 0.9234 (m-30) cc_final: 0.8924 (p0) REVERT: E 79 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.6814 (tttt) REVERT: F 88 TYR cc_start: 0.9111 (m-10) cc_final: 0.8873 (m-10) REVERT: G 39 TYR cc_start: 0.9427 (m-80) cc_final: 0.8869 (m-80) REVERT: G 56 GLU cc_start: 0.9336 (tt0) cc_final: 0.9028 (tt0) REVERT: G 90 ASP cc_start: 0.8682 (t0) cc_final: 0.8283 (t0) REVERT: G 92 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8534 (tt0) REVERT: H 42 TYR cc_start: 0.8978 (t80) cc_final: 0.8774 (t80) REVERT: H 83 TYR cc_start: 0.8194 (m-10) cc_final: 0.7224 (m-10) REVERT: H 93 GLU cc_start: 0.9017 (mp0) cc_final: 0.8699 (mp0) REVERT: A 667 PHE cc_start: 0.8500 (m-80) cc_final: 0.8290 (m-80) REVERT: A 669 GLU cc_start: 0.8228 (pp20) cc_final: 0.7592 (tm-30) REVERT: A 673 LYS cc_start: 0.8802 (pttp) cc_final: 0.8561 (pttm) REVERT: A 674 GLU cc_start: 0.8950 (pp20) cc_final: 0.8649 (pt0) REVERT: A 680 MET cc_start: 0.8470 (ttm) cc_final: 0.8219 (ttm) REVERT: A 682 LYS cc_start: 0.9304 (mmmt) cc_final: 0.8953 (mmmt) REVERT: B 680 MET cc_start: 0.6906 (tpt) cc_final: 0.5987 (ptp) REVERT: R 110 GLN cc_start: 0.2812 (OUTLIER) cc_final: 0.2423 (tp40) outliers start: 22 outliers final: 11 residues processed: 280 average time/residue: 0.2936 time to fit residues: 114.5173 Evaluate side-chains 265 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 252 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 90 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 Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 117 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.067508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.044000 restraints weight = 67917.738| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.37 r_work: 0.2707 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14974 Z= 0.173 Angle : 0.595 8.620 21501 Z= 0.341 Chirality : 0.035 0.146 2449 Planarity : 0.004 0.033 1707 Dihedral : 29.335 171.506 4352 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.62 % Allowed : 17.60 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.27), residues: 1013 helix: 2.02 (0.20), residues: 648 sheet: -1.07 (0.73), residues: 48 loop : -0.50 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP R 36 HIS 0.006 0.001 HIS R 78 PHE 0.020 0.002 PHE R 72 TYR 0.019 0.001 TYR G 57 ARG 0.005 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 842) hydrogen bonds : angle 3.28772 ( 2144) metal coordination : bond 0.01198 ( 16) metal coordination : angle 2.76403 ( 18) covalent geometry : bond 0.00387 (14957) covalent geometry : angle 0.58936 (21483) Misc. bond : bond 0.00040 ( 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 285 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 263 time to evaluate : 1.142 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: 0.9030 (pm20) cc_final: 0.8503 (pm20) REVERT: C 39 TYR cc_start: 0.8849 (m-80) cc_final: 0.8516 (m-80) REVERT: D 43 LYS cc_start: 0.9655 (OUTLIER) cc_final: 0.9446 (mttp) REVERT: D 90 THR cc_start: 0.9539 (p) cc_final: 0.9238 (p) REVERT: D 93 GLU cc_start: 0.9053 (mp0) cc_final: 0.8727 (mp0) REVERT: E 77 ASP cc_start: 0.9222 (m-30) cc_final: 0.8986 (p0) REVERT: E 79 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7177 (mtpt) REVERT: F 85 ASP cc_start: 0.8800 (m-30) cc_final: 0.8391 (m-30) REVERT: G 39 TYR cc_start: 0.9431 (m-80) cc_final: 0.8867 (m-80) REVERT: G 56 GLU cc_start: 0.9334 (tt0) cc_final: 0.9015 (tt0) REVERT: G 90 ASP cc_start: 0.8682 (t0) cc_final: 0.8235 (t0) REVERT: H 42 TYR cc_start: 0.8922 (t80) cc_final: 0.8626 (t80) REVERT: H 44 VAL cc_start: 0.9784 (t) cc_final: 0.9574 (p) REVERT: H 93 GLU cc_start: 0.9073 (mp0) cc_final: 0.8684 (mp0) REVERT: A 661 LYS cc_start: 0.8405 (ttmt) cc_final: 0.7838 (mttm) REVERT: A 667 PHE cc_start: 0.8646 (m-80) cc_final: 0.8416 (m-80) REVERT: A 669 GLU cc_start: 0.8283 (pp20) cc_final: 0.7701 (tm-30) REVERT: A 673 LYS cc_start: 0.8784 (pttp) cc_final: 0.8569 (pttm) REVERT: A 674 GLU cc_start: 0.9063 (pp20) cc_final: 0.8764 (pt0) REVERT: A 680 MET cc_start: 0.8383 (ttm) cc_final: 0.8130 (ttm) REVERT: A 682 LYS cc_start: 0.9355 (mmmt) cc_final: 0.9003 (mmmt) REVERT: B 695 LEU cc_start: 0.7232 (tt) cc_final: 0.6823 (mp) REVERT: R 36 TRP cc_start: 0.5285 (m100) cc_final: 0.5001 (m100) REVERT: R 110 GLN cc_start: 0.2575 (OUTLIER) cc_final: 0.2132 (tp40) outliers start: 22 outliers final: 14 residues processed: 273 average time/residue: 0.2835 time to fit residues: 108.8995 Evaluate side-chains 268 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 251 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 44 LYS Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 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 B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 102 VAL Chi-restraints excluded: chain R residue 110 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 15 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 121 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN E 68 GLN E 85 GLN ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.065524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041933 restraints weight = 66866.167| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.37 r_work: 0.2643 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14974 Z= 0.265 Angle : 0.651 8.703 21501 Z= 0.370 Chirality : 0.038 0.152 2449 Planarity : 0.004 0.039 1707 Dihedral : 29.884 170.979 4352 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.04 % Allowed : 18.07 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.27), residues: 1013 helix: 1.87 (0.20), residues: 648 sheet: -0.64 (0.79), residues: 47 loop : -0.66 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP R 149 HIS 0.012 0.002 HIS R 133 PHE 0.024 0.002 PHE R 13 TYR 0.014 0.002 TYR D 121 ARG 0.005 0.001 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 842) hydrogen bonds : angle 3.54414 ( 2144) metal coordination : bond 0.02103 ( 16) metal coordination : angle 3.94881 ( 18) covalent geometry : bond 0.00595 (14957) covalent geometry : angle 0.64124 (21483) Misc. bond : bond 0.00124 ( 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 284 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 250 time to evaluate : 1.151 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 105 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8997 (mt-10) REVERT: D 43 LYS cc_start: 0.9724 (OUTLIER) cc_final: 0.9502 (mttp) REVERT: D 79 ARG cc_start: 0.9087 (ttm-80) cc_final: 0.8865 (ttp-110) REVERT: D 90 THR cc_start: 0.9537 (p) cc_final: 0.9095 (p) REVERT: D 93 GLU cc_start: 0.9144 (mp0) cc_final: 0.8789 (mp0) REVERT: E 79 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7355 (mttt) REVERT: F 59 LYS cc_start: 0.9292 (ptmt) cc_final: 0.9058 (ttpt) REVERT: G 56 GLU cc_start: 0.9308 (tt0) cc_final: 0.8985 (tt0) REVERT: G 90 ASP cc_start: 0.8706 (t0) cc_final: 0.8206 (t0) REVERT: G 92 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8385 (tt0) REVERT: H 42 TYR cc_start: 0.8935 (t80) cc_final: 0.8590 (t80) REVERT: H 76 GLU cc_start: 0.9245 (tp30) cc_final: 0.8827 (tp30) REVERT: H 93 GLU cc_start: 0.9146 (mp0) cc_final: 0.8660 (mp0) REVERT: A 669 GLU cc_start: 0.8382 (pp20) cc_final: 0.7799 (tm-30) REVERT: A 674 GLU cc_start: 0.9138 (pp20) cc_final: 0.8761 (pt0) REVERT: A 680 MET cc_start: 0.8284 (ttm) cc_final: 0.7908 (ttm) REVERT: A 681 ARG cc_start: 0.8600 (ptp90) cc_final: 0.8361 (ptp90) REVERT: A 682 LYS cc_start: 0.9262 (mmmt) cc_final: 0.9014 (mmmt) REVERT: B 680 MET cc_start: 0.6944 (tpt) cc_final: 0.5750 (ptp) REVERT: B 695 LEU cc_start: 0.6791 (tt) cc_final: 0.6382 (mt) outliers start: 34 outliers final: 22 residues processed: 269 average time/residue: 0.2863 time to fit residues: 107.5084 Evaluate side-chains 265 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 46 VAL Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 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 F residue 62 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 A residue 699 HIS Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 24 VAL Chi-restraints excluded: chain R residue 53 PHE Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 49 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 32 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 76 GLN G 73 ASN ** R 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.066886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.044607 restraints weight = 68643.083| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.29 r_work: 0.2721 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14974 Z= 0.146 Angle : 0.596 10.871 21501 Z= 0.341 Chirality : 0.035 0.148 2449 Planarity : 0.004 0.037 1707 Dihedral : 29.341 168.968 4349 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.02 % Allowed : 21.17 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.27), residues: 1013 helix: 2.08 (0.20), residues: 647 sheet: -0.53 (0.78), residues: 47 loop : -0.59 (0.35), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP R 149 HIS 0.003 0.001 HIS R 133 PHE 0.022 0.001 PHE R 13 TYR 0.017 0.001 TYR H 83 ARG 0.006 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 842) hydrogen bonds : angle 3.28926 ( 2144) metal coordination : bond 0.00837 ( 16) metal coordination : angle 2.39863 ( 18) covalent geometry : bond 0.00320 (14957) covalent geometry : angle 0.59208 (21483) Misc. bond : bond 0.00012 ( 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 278 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 261 time to evaluate : 1.180 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: 0.8972 (pm20) cc_final: 0.8417 (pm20) REVERT: C 38 ASN cc_start: 0.9109 (m-40) cc_final: 0.8846 (t0) REVERT: D 90 THR cc_start: 0.9545 (p) cc_final: 0.9125 (p) REVERT: D 93 GLU cc_start: 0.9101 (mp0) cc_final: 0.8769 (mp0) REVERT: D 116 LYS cc_start: 0.9447 (ttpp) cc_final: 0.9192 (tmtt) REVERT: E 79 LYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7668 (mttt) REVERT: E 90 MET cc_start: 0.9303 (mmm) cc_final: 0.9073 (mmm) REVERT: F 59 LYS cc_start: 0.9195 (ptmt) cc_final: 0.8944 (ttpt) REVERT: F 84 MET cc_start: 0.9142 (mmm) cc_final: 0.8714 (tpp) REVERT: G 56 GLU cc_start: 0.9248 (tt0) cc_final: 0.8957 (tt0) REVERT: G 90 ASP cc_start: 0.8650 (t0) cc_final: 0.8114 (t0) REVERT: A 669 GLU cc_start: 0.8453 (pp20) cc_final: 0.7689 (tm-30) REVERT: A 673 LYS cc_start: 0.8730 (pttm) cc_final: 0.8434 (pttm) REVERT: A 674 GLU cc_start: 0.9182 (pp20) cc_final: 0.8842 (pt0) REVERT: A 680 MET cc_start: 0.8427 (ttm) cc_final: 0.8081 (ttm) REVERT: A 682 LYS cc_start: 0.9265 (mmmt) cc_final: 0.8881 (mmmt) REVERT: B 658 MET cc_start: 0.5276 (tmm) cc_final: 0.5054 (ppp) REVERT: B 680 MET cc_start: 0.6801 (tpt) cc_final: 0.5775 (ptp) outliers start: 17 outliers final: 10 residues processed: 268 average time/residue: 0.2819 time to fit residues: 105.8281 Evaluate side-chains 261 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 250 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 76 GLN 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 111 VAL Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 42 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 107 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN E 68 GLN E 76 GLN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.067323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.044222 restraints weight = 70161.312| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.36 r_work: 0.2722 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14974 Z= 0.154 Angle : 0.601 9.717 21501 Z= 0.343 Chirality : 0.035 0.153 2449 Planarity : 0.004 0.046 1707 Dihedral : 29.317 169.036 4349 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.14 % Allowed : 22.24 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.27), residues: 1013 helix: 2.14 (0.20), residues: 648 sheet: -0.52 (0.78), residues: 47 loop : -0.62 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP R 149 HIS 0.003 0.001 HIS F 75 PHE 0.024 0.002 PHE R 13 TYR 0.018 0.002 TYR H 83 ARG 0.007 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 842) hydrogen bonds : angle 3.35256 ( 2144) metal coordination : bond 0.00921 ( 16) metal coordination : angle 2.28549 ( 18) covalent geometry : bond 0.00341 (14957) covalent geometry : angle 0.59803 (21483) Misc. bond : bond 0.00029 ( 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 278 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 1.268 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: 0.8971 (pm20) cc_final: 0.8432 (pm20) REVERT: L 24 ASP cc_start: 0.8698 (t0) cc_final: 0.8488 (t0) REVERT: D 31 ARG cc_start: 0.5015 (tpm170) cc_final: 0.4702 (tpm170) REVERT: D 90 THR cc_start: 0.9550 (p) cc_final: 0.9146 (p) REVERT: D 93 GLU cc_start: 0.9111 (mp0) cc_final: 0.8801 (mp0) REVERT: E 79 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8159 (mttt) REVERT: E 90 MET cc_start: 0.9344 (mmm) cc_final: 0.9132 (mmm) REVERT: F 59 LYS cc_start: 0.9210 (ptmt) cc_final: 0.8985 (ttpt) REVERT: G 56 GLU cc_start: 0.9344 (tt0) cc_final: 0.8943 (tt0) REVERT: G 90 ASP cc_start: 0.8666 (t0) cc_final: 0.8143 (t0) REVERT: H 34 LYS cc_start: 0.6669 (tttp) cc_final: 0.6435 (tptt) REVERT: H 93 GLU cc_start: 0.9093 (mp0) cc_final: 0.8667 (mp0) REVERT: A 661 LYS cc_start: 0.8363 (tttt) cc_final: 0.7486 (mtmt) REVERT: A 669 GLU cc_start: 0.8573 (pp20) cc_final: 0.7759 (tm-30) REVERT: A 674 GLU cc_start: 0.9202 (pp20) cc_final: 0.8870 (pt0) REVERT: A 680 MET cc_start: 0.8494 (ttm) cc_final: 0.8094 (ttm) REVERT: A 681 ARG cc_start: 0.8523 (ptp90) cc_final: 0.8316 (ptp90) REVERT: A 682 LYS cc_start: 0.9259 (mmmt) cc_final: 0.9034 (mmmt) REVERT: B 695 LEU cc_start: 0.7408 (tp) cc_final: 0.7035 (mt) REVERT: R 100 TYR cc_start: 0.6689 (t80) cc_final: 0.5986 (t80) outliers start: 18 outliers final: 12 residues processed: 269 average time/residue: 0.2747 time to fit residues: 104.8783 Evaluate side-chains 261 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 248 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN 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 111 VAL Chi-restraints excluded: chain B residue 685 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain R residue 65 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 85 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 chunk 111 optimal weight: 0.0670 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 ASN E 68 GLN G 73 ASN R 133 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.067939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.045272 restraints weight = 69124.920| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 3.31 r_work: 0.2752 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14974 Z= 0.148 Angle : 0.615 9.283 21501 Z= 0.347 Chirality : 0.035 0.162 2449 Planarity : 0.004 0.037 1707 Dihedral : 29.173 168.544 4349 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.90 % Allowed : 23.19 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.27), residues: 1013 helix: 2.10 (0.20), residues: 647 sheet: -0.61 (0.80), residues: 48 loop : -0.59 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.004 TRP R 149 HIS 0.025 0.001 HIS R 133 PHE 0.024 0.001 PHE R 13 TYR 0.022 0.001 TYR R 137 ARG 0.007 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03619 ( 842) hydrogen bonds : angle 3.36258 ( 2144) metal coordination : bond 0.00733 ( 16) metal coordination : angle 2.09518 ( 18) covalent geometry : bond 0.00328 (14957) covalent geometry : angle 0.61241 (21483) Misc. bond : bond 0.00017 ( 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 278 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 262 time to evaluate : 1.234 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: 0.8892 (pm20) cc_final: 0.8373 (pm20) REVERT: L 24 ASP cc_start: 0.8841 (t0) cc_final: 0.8562 (t0) REVERT: L 84 MET cc_start: 0.9449 (mmm) cc_final: 0.8951 (mmm) REVERT: L 85 ASP cc_start: 0.9070 (m-30) cc_final: 0.8820 (m-30) REVERT: D 31 ARG cc_start: 0.5136 (tpm170) cc_final: 0.4868 (tpm170) REVERT: D 90 THR cc_start: 0.9532 (p) cc_final: 0.9137 (p) REVERT: D 93 GLU cc_start: 0.9052 (mp0) cc_final: 0.8784 (mp0) REVERT: D 116 LYS cc_start: 0.9406 (ttpp) cc_final: 0.9164 (tmtt) REVERT: E 79 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7864 (mttt) REVERT: E 90 MET cc_start: 0.9285 (mmm) cc_final: 0.9042 (mmm) REVERT: F 59 LYS cc_start: 0.9213 (ptmt) cc_final: 0.9001 (ttpt) REVERT: F 84 MET cc_start: 0.9094 (mmm) cc_final: 0.8720 (tpp) REVERT: G 90 ASP cc_start: 0.8654 (t0) cc_final: 0.8048 (t0) REVERT: G 92 GLU cc_start: 0.8528 (tt0) cc_final: 0.8318 (tt0) REVERT: H 93 GLU cc_start: 0.9048 (mp0) cc_final: 0.8622 (mp0) REVERT: A 669 GLU cc_start: 0.8559 (pp20) cc_final: 0.7733 (tm-30) REVERT: A 674 GLU cc_start: 0.9214 (pp20) cc_final: 0.8875 (pt0) REVERT: A 680 MET cc_start: 0.8528 (ttm) cc_final: 0.8124 (ttm) REVERT: A 682 LYS cc_start: 0.9245 (mmmt) cc_final: 0.8908 (mmmt) REVERT: B 695 LEU cc_start: 0.7237 (tp) cc_final: 0.6894 (mt) REVERT: R 100 TYR cc_start: 0.6627 (t80) cc_final: 0.6101 (t80) REVERT: R 129 LEU cc_start: 0.5126 (tp) cc_final: 0.4061 (mt) outliers start: 16 outliers final: 11 residues processed: 267 average time/residue: 0.2760 time to fit residues: 104.3311 Evaluate side-chains 268 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 256 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain H residue 90 THR 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 65 ASN Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 133 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 99 optimal weight: 20.0000 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 52 optimal weight: 20.0000 chunk 48 optimal weight: 0.1980 chunk 120 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.068512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.045691 restraints weight = 69123.671| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 3.31 r_work: 0.2766 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14974 Z= 0.148 Angle : 0.635 11.526 21501 Z= 0.352 Chirality : 0.035 0.151 2449 Planarity : 0.004 0.037 1707 Dihedral : 29.123 168.466 4349 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.43 % Allowed : 24.49 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.27), residues: 1013 helix: 2.08 (0.20), residues: 648 sheet: -0.82 (0.77), residues: 49 loop : -0.65 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP R 36 HIS 0.023 0.001 HIS R 133 PHE 0.021 0.002 PHE R 13 TYR 0.026 0.002 TYR G 57 ARG 0.007 0.000 ARG H 99 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 842) hydrogen bonds : angle 3.36265 ( 2144) metal coordination : bond 0.00714 ( 16) metal coordination : angle 2.08788 ( 18) covalent geometry : bond 0.00328 (14957) covalent geometry : angle 0.63253 (21483) Misc. bond : bond 0.00008 ( 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 273 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 261 time to evaluate : 1.139 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: symmetry clash REVERT: K 59 GLU cc_start: 0.8854 (pm20) cc_final: 0.8365 (pm20) REVERT: L 85 ASP cc_start: 0.9072 (m-30) cc_final: 0.8803 (m-30) REVERT: D 31 ARG cc_start: 0.5125 (tpm170) cc_final: 0.4844 (tpm170) REVERT: D 90 THR cc_start: 0.9536 (p) cc_final: 0.9163 (p) REVERT: D 93 GLU cc_start: 0.9045 (mp0) cc_final: 0.8798 (mp0) REVERT: E 79 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7914 (mmmt) REVERT: E 90 MET cc_start: 0.9281 (mmm) cc_final: 0.9032 (mmm) REVERT: F 59 LYS cc_start: 0.9196 (ptmt) cc_final: 0.8996 (ttpt) REVERT: F 84 MET cc_start: 0.9118 (mmm) cc_final: 0.8868 (tpp) REVERT: G 90 ASP cc_start: 0.8662 (t0) cc_final: 0.8103 (t0) REVERT: G 92 GLU cc_start: 0.8498 (tt0) cc_final: 0.8266 (tt0) REVERT: H 34 LYS cc_start: 0.6679 (tptt) cc_final: 0.6066 (tppt) REVERT: H 93 GLU cc_start: 0.9023 (mp0) cc_final: 0.8611 (mp0) REVERT: A 658 MET cc_start: 0.8074 (tpp) cc_final: 0.7848 (tpt) REVERT: A 669 GLU cc_start: 0.8590 (pp20) cc_final: 0.7754 (tm-30) REVERT: A 673 LYS cc_start: 0.8678 (pttm) cc_final: 0.8360 (pttm) REVERT: A 680 MET cc_start: 0.8489 (ttm) cc_final: 0.8069 (ttm) REVERT: A 681 ARG cc_start: 0.8663 (ptp90) cc_final: 0.8168 (ptp90) REVERT: A 682 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8890 (mmmt) REVERT: B 695 LEU cc_start: 0.7228 (tp) cc_final: 0.6860 (mt) REVERT: R 76 MET cc_start: 0.4933 (mpp) cc_final: 0.3652 (ppp) REVERT: R 100 TYR cc_start: 0.6654 (t80) cc_final: 0.6181 (t80) REVERT: R 129 LEU cc_start: 0.5107 (tp) cc_final: 0.4092 (mt) outliers start: 12 outliers final: 10 residues processed: 264 average time/residue: 0.2770 time to fit residues: 103.2700 Evaluate side-chains 264 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 253 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain F residue 58 LEU 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 698 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 65 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 71 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 20 optimal weight: 0.1980 chunk 120 optimal weight: 0.0050 chunk 106 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 GLN R 133 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.068111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.045114 restraints weight = 69690.143| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.33 r_work: 0.2754 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14974 Z= 0.157 Angle : 0.642 10.496 21501 Z= 0.356 Chirality : 0.035 0.148 2449 Planarity : 0.004 0.040 1707 Dihedral : 29.150 168.593 4349 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.90 % Allowed : 24.02 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.27), residues: 1013 helix: 2.10 (0.21), residues: 648 sheet: -0.84 (0.77), residues: 49 loop : -0.65 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP R 36 HIS 0.022 0.001 HIS R 133 PHE 0.022 0.001 PHE R 13 TYR 0.027 0.002 TYR G 57 ARG 0.007 0.000 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.03624 ( 842) hydrogen bonds : angle 3.39061 ( 2144) metal coordination : bond 0.00855 ( 16) metal coordination : angle 2.02306 ( 18) covalent geometry : bond 0.00352 (14957) covalent geometry : angle 0.63978 (21483) Misc. bond : bond 0.00023 ( 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 270 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 254 time to evaluate : 1.155 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: K 59 GLU cc_start: 0.8857 (pm20) cc_final: 0.8366 (pm20) REVERT: L 24 ASP cc_start: 0.8668 (t0) cc_final: 0.8451 (t0) REVERT: L 85 ASP cc_start: 0.9085 (m-30) cc_final: 0.8846 (m-30) REVERT: C 38 ASN cc_start: 0.8983 (t0) cc_final: 0.8765 (t0) REVERT: D 31 ARG cc_start: 0.5039 (tpm170) cc_final: 0.4733 (tpm170) REVERT: D 79 ARG cc_start: 0.9215 (ttm-80) cc_final: 0.8875 (ttm-80) REVERT: D 90 THR cc_start: 0.9513 (p) cc_final: 0.9092 (p) REVERT: D 93 GLU cc_start: 0.9038 (mp0) cc_final: 0.8799 (mp0) REVERT: E 79 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7966 (mmmt) REVERT: E 90 MET cc_start: 0.9297 (mmm) cc_final: 0.9044 (mmm) REVERT: F 84 MET cc_start: 0.9103 (mmm) cc_final: 0.8783 (tpp) REVERT: G 90 ASP cc_start: 0.8685 (t0) cc_final: 0.8159 (t0) REVERT: G 92 GLU cc_start: 0.8497 (tt0) cc_final: 0.8261 (tt0) REVERT: H 34 LYS cc_start: 0.6459 (tptt) cc_final: 0.5786 (tppt) REVERT: H 35 GLU cc_start: 0.6116 (tp30) cc_final: 0.5671 (tp30) REVERT: H 93 GLU cc_start: 0.9024 (mp0) cc_final: 0.8609 (mp0) REVERT: A 669 GLU cc_start: 0.8591 (pp20) cc_final: 0.7827 (tm-30) REVERT: A 673 LYS cc_start: 0.8697 (pttm) cc_final: 0.8388 (pttm) REVERT: A 680 MET cc_start: 0.8530 (ttm) cc_final: 0.7523 (tmm) REVERT: A 681 ARG cc_start: 0.8665 (ptp90) cc_final: 0.8154 (ptp90) REVERT: A 682 LYS cc_start: 0.9264 (mmmt) cc_final: 0.8794 (mmmt) REVERT: B 695 LEU cc_start: 0.7157 (tp) cc_final: 0.6893 (mt) REVERT: R 76 MET cc_start: 0.4920 (mpp) cc_final: 0.3525 (ppp) REVERT: R 100 TYR cc_start: 0.6500 (t80) cc_final: 0.6230 (t80) REVERT: R 129 LEU cc_start: 0.5238 (tp) cc_final: 0.4173 (mt) outliers start: 16 outliers final: 13 residues processed: 259 average time/residue: 0.2688 time to fit residues: 98.7881 Evaluate side-chains 266 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 68 GLN Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain F residue 58 LEU 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 698 VAL Chi-restraints excluded: chain R residue 57 LEU Chi-restraints excluded: chain R residue 65 ASN Chi-restraints excluded: chain R residue 72 PHE Chi-restraints excluded: chain R residue 93 GLN 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 114 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 52 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** R 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.065173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.042334 restraints weight = 68445.506| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.35 r_work: 0.2651 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 14974 Z= 0.292 Angle : 0.725 10.992 21501 Z= 0.399 Chirality : 0.041 0.266 2449 Planarity : 0.005 0.041 1707 Dihedral : 29.759 169.444 4349 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.43 % Allowed : 24.26 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.27), residues: 1013 helix: 1.82 (0.20), residues: 648 sheet: -0.83 (0.75), residues: 49 loop : -0.79 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP R 36 HIS 0.016 0.002 HIS R 133 PHE 0.028 0.002 PHE R 13 TYR 0.037 0.002 TYR G 57 ARG 0.007 0.001 ARG D 99 Details of bonding type rmsd hydrogen bonds : bond 0.05163 ( 842) hydrogen bonds : angle 3.78384 ( 2144) metal coordination : bond 0.02055 ( 16) metal coordination : angle 3.59875 ( 18) covalent geometry : bond 0.00662 (14957) covalent geometry : angle 0.71782 (21483) Misc. bond : bond 0.00121 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7791.34 seconds wall clock time: 133 minutes 19.39 seconds (7999.39 seconds total)