Starting phenix.real_space_refine on Fri Jun 13 03:55:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iej_35383/06_2025/8iej_35383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iej_35383/06_2025/8iej_35383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iej_35383/06_2025/8iej_35383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iej_35383/06_2025/8iej_35383.map" model { file = "/net/cci-nas-00/data/ceres_data/8iej_35383/06_2025/8iej_35383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iej_35383/06_2025/8iej_35383.cif" } resolution = 3.12 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 Anisotropic ADP refinement not supported. Converting 1067 atoms to isotropic. 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 35 5.16 5 C 7937 2.51 5 N 2635 2.21 5 O 3181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14086 Number of models: 1 Model: "" Number of chains: 15 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: "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: "A" Number of atoms: 476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 476 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 57} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 494 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain: "R" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1067 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 135} Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 172 Unresolved non-hydrogen dihedrals: 117 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 105 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: "M" 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 12108 SG CYS A 948 47.191 47.637 12.094 1.00216.57 S ATOM 12259 SG CYS A 968 47.274 50.753 11.972 1.00213.80 S ATOM 12285 SG CYS A 971 44.012 50.383 11.912 1.00208.87 S ATOM 12214 SG CYS A 963 43.787 45.876 27.411 1.00197.39 S ATOM 12386 SG CYS A 983 41.373 46.465 23.589 1.00200.37 S ATOM 12587 SG CYS M 922 63.805 58.535 26.486 1.00185.29 S ATOM 12606 SG CYS M 925 67.390 57.651 27.123 1.00189.09 S ATOM 12746 SG CYS M 942 64.428 55.921 29.187 1.00161.27 S ATOM 12772 SG CYS M 945 65.569 58.880 30.124 1.00148.39 S ATOM 12701 SG CYS M 937 53.818 64.915 26.888 1.00146.39 S ATOM 12879 SG CYS M 957 57.040 66.699 27.510 1.00142.03 S ATOM 12901 SG CYS M 960 54.070 68.660 26.301 1.00148.06 S Time building chain proxies: 8.64, per 1000 atoms: 0.61 Number of scatterers: 14086 At special positions: 0 Unit cell: (120.288, 121.362, 113.844, 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 35 16.00 P 294 15.00 O 3181 8.00 N 2635 7.00 C 7937 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.79 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 948 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 971 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 968 " pdb=" ZN A1102 " pdb="ZN ZN A1102 " - pdb=" NE2 HIS A 965 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 983 " pdb="ZN ZN A1102 " - pdb=" SG CYS A 963 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 945 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 942 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 925 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 922 " pdb=" ZN M1002 " pdb="ZN ZN M1002 " - pdb=" ND1 HIS M 939 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 957 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 960 " pdb="ZN ZN M1002 " - pdb=" SG CYS M 937 " Number of angles added : 9 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 13 sheets defined 62.2% alpha, 5.0% beta 140 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 6.60 Creating SS restraints... Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.473A 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: 3.542A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 124 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.874A 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 49 through 76 removed outlier: 3.786A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.661A 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 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.535A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 74 removed outlier: 4.425A 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 removed outlier: 3.605A pdb=" N ALA H 107 " --> pdb=" O PRO H 103 " (cutoff:3.500A) 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 132 removed outlier: 3.557A 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: 4.171A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP L 68 " --> pdb=" O ASN L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'A' and resid 942 through 947 Processing helix chain 'A' and resid 969 through 978 Processing helix chain 'M' and resid 916 through 920 Processing helix chain 'M' and resid 942 through 952 Processing helix chain 'R' and resid 3 through 19 Processing helix chain 'R' and resid 89 through 94 Processing helix chain 'R' and resid 101 through 115 Processing helix chain 'R' and resid 123 through 133 Processing helix chain 'R' and resid 133 through 149 removed outlier: 3.562A pdb=" N TRP R 149 " --> pdb=" O VAL R 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.192A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA3, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.822A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.924A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.395A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'G' and resid 101 through 102 removed outlier: 6.791A pdb=" N THR G 101 " --> pdb=" O TYR L 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.809A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AB2, first strand: chain 'A' and resid 966 through 967 removed outlier: 4.103A pdb=" N VAL A 959 " --> pdb=" O HIS A 996 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N HIS A 996 " --> pdb=" O VAL A 959 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 939 through 941 removed outlier: 3.727A pdb=" N HIS M 939 " --> pdb=" O LEU M 934 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 24 through 28 483 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 361 hydrogen bonds 718 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 5.43 Time building geometry restraints manager: 4.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3044 1.33 - 1.45: 4483 1.45 - 1.57: 6786 1.57 - 1.69: 586 1.69 - 1.81: 48 Bond restraints: 14947 Sorted by residual: bond pdb=" CA ARG A 981 " pdb=" C ARG A 981 " ideal model delta sigma weight residual 1.524 1.503 0.021 1.35e-02 5.49e+03 2.41e+00 bond pdb=" CB ARG D 79 " pdb=" CG ARG D 79 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CA CYS A 971 " pdb=" C CYS A 971 " ideal model delta sigma weight residual 1.524 1.541 -0.017 1.29e-02 6.01e+03 1.80e+00 bond pdb=" CG1 ILE F 50 " pdb=" CD1 ILE F 50 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.78e+00 bond pdb=" CB GLU L 53 " pdb=" CG GLU L 53 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.71e+00 ... (remaining 14942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 21333 2.62 - 5.25: 118 5.25 - 7.87: 12 7.87 - 10.50: 1 10.50 - 13.12: 1 Bond angle restraints: 21465 Sorted by residual: angle pdb=" N ARG A 981 " pdb=" CA ARG A 981 " pdb=" C ARG A 981 " ideal model delta sigma weight residual 108.17 95.05 13.12 1.85e+00 2.92e-01 5.03e+01 angle pdb=" N LYS A 955 " pdb=" CA LYS A 955 " pdb=" C LYS A 955 " ideal model delta sigma weight residual 110.28 115.76 -5.48 1.48e+00 4.57e-01 1.37e+01 angle pdb=" C GLU R 132 " pdb=" N ASN R 133 " pdb=" CA ASN R 133 " ideal model delta sigma weight residual 122.76 117.06 5.70 1.63e+00 3.76e-01 1.22e+01 angle pdb=" CB ARG R 11 " pdb=" CG ARG R 11 " pdb=" CD ARG R 11 " ideal model delta sigma weight residual 111.30 119.23 -7.93 2.30e+00 1.89e-01 1.19e+01 angle pdb=" N ARG M 928 " pdb=" CA ARG M 928 " pdb=" C ARG M 928 " ideal model delta sigma weight residual 108.34 112.71 -4.37 1.31e+00 5.83e-01 1.11e+01 ... (remaining 21460 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.03: 6767 34.03 - 68.06: 1449 68.06 - 102.10: 15 102.10 - 136.13: 1 136.13 - 170.16: 3 Dihedral angle restraints: 8235 sinusoidal: 5233 harmonic: 3002 Sorted by residual: dihedral pdb=" CA ARG M 928 " pdb=" C ARG M 928 " pdb=" N LYS M 929 " pdb=" CA LYS M 929 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO R 28 " pdb=" C PRO R 28 " pdb=" N SER R 29 " pdb=" CA SER R 29 " ideal model delta harmonic sigma weight residual 180.00 159.93 20.07 0 5.00e+00 4.00e-02 1.61e+01 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 49.84 170.16 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 8232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2140 0.059 - 0.119: 269 0.119 - 0.178: 21 0.178 - 0.237: 1 0.237 - 0.296: 1 Chirality restraints: 2432 Sorted by residual: chirality pdb=" CA ARG A 981 " pdb=" N ARG A 981 " pdb=" C ARG A 981 " pdb=" CB ARG A 981 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ARG A 979 " pdb=" N ARG A 979 " pdb=" C ARG A 979 " pdb=" CB ARG A 979 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.30e-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 2.34 0.17 2.00e-01 2.50e+01 7.39e-01 ... (remaining 2429 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.025 2.00e-02 2.50e+03 3.06e-02 1.87e+01 pdb=" CG TYR D 83 " 0.074 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 36 " -0.020 2.00e-02 2.50e+03 1.82e-02 8.26e+00 pdb=" CG TRP R 36 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP R 36 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP R 36 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 36 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 36 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 36 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 36 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 36 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 36 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 17 " -0.026 2.00e-02 2.50e+03 1.15e-02 3.63e+00 pdb=" N9 DA I 17 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DA I 17 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 17 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I 17 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 17 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 17 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 17 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 17 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 17 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I 17 " 0.001 2.00e-02 2.50e+03 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 3 2.12 - 2.81: 3438 2.81 - 3.51: 20074 3.51 - 4.20: 39166 4.20 - 4.90: 58629 Nonbonded interactions: 121310 Sorted by model distance: nonbonded pdb=" OH TYR A 999 " pdb=" NE2 HIS M 939 " model vdw 1.421 3.120 nonbonded pdb=" OH TYR A 999 " pdb=" CD2 HIS M 939 " model vdw 1.627 3.260 nonbonded pdb=" NH2 ARG A 954 " pdb=" SG CYS A 971 " model vdw 2.095 3.480 nonbonded pdb=" OH TYR C 50 " pdb=" OE1 GLN D 95 " model vdw 2.132 3.040 nonbonded pdb=" OG SER R 29 " pdb=" O ASN R 32 " model vdw 2.136 3.040 ... (remaining 121305 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 942 through 952 or resid 954 through 972 or resid 975 thro \ ugh 976 or resid 979 through 992 or resid 994 through 1000 or resid 1101 through \ 1102)) selection = (chain 'M' and (resid 916 through 925 or (resid 926 and (name N or name CA or na \ me C or name O or name CB )) or resid 928 through 929 or (resid 930 and (name N \ or name CA or name C or name O or name CB )) or resid 931 through 946 or resid 9 \ 49 through 950 or resid 953 through 966 or resid 968 through 973 or (resid 974 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1001 through 10 \ 02)) } 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=0.27 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.780 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.010 0.585 14963 Z= 0.488 Angle : 0.660 18.310 21474 Z= 0.383 Chirality : 0.040 0.296 2432 Planarity : 0.005 0.066 1710 Dihedral : 26.500 170.160 6293 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.32 % Allowed : 0.60 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.90 (0.27), residues: 1008 helix: 2.04 (0.21), residues: 641 sheet: 0.59 (1.02), residues: 27 loop : -0.17 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.005 TRP R 36 HIS 0.006 0.001 HIS A 996 PHE 0.020 0.002 PHE M 941 TYR 0.074 0.002 TYR D 83 ARG 0.011 0.001 ARG R 11 Details of bonding type rmsd hydrogen bonds : bond 0.09008 ( 844) hydrogen bonds : angle 3.88644 ( 2146) metal coordination : bond 0.24229 ( 14) metal coordination : angle 8.34178 ( 9) covalent geometry : bond 0.00551 (14947) covalent geometry : angle 0.63806 (21465) Misc. bond : bond 0.29501 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 1.084 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: C 38 ASN cc_start: 0.8421 (t0) cc_final: 0.8127 (p0) REVERT: C 72 ASP cc_start: 0.8554 (m-30) cc_final: 0.8333 (m-30) REVERT: C 90 ASP cc_start: 0.8660 (t70) cc_final: 0.8449 (t0) REVERT: D 68 ASP cc_start: 0.8827 (t70) cc_final: 0.8595 (t0) REVERT: G 24 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8961 (mm-40) REVERT: G 38 ASN cc_start: 0.8356 (t0) cc_final: 0.7963 (t0) REVERT: G 90 ASP cc_start: 0.8512 (t70) cc_final: 0.8301 (t70) REVERT: K 56 LYS cc_start: 0.9346 (ttmm) cc_final: 0.9120 (ttpp) REVERT: K 59 GLU cc_start: 0.8638 (pm20) cc_final: 0.8309 (pm20) REVERT: A 972 VAL cc_start: 0.9370 (m) cc_final: 0.9048 (m) REVERT: A 996 HIS cc_start: 0.6472 (t-90) cc_final: 0.6202 (t-90) REVERT: M 938 PHE cc_start: 0.9013 (m-80) cc_final: 0.8619 (m-80) REVERT: M 967 ASN cc_start: 0.9247 (m-40) cc_final: 0.8770 (m-40) REVERT: R 36 TRP cc_start: 0.6377 (m100) cc_final: 0.5977 (m100) outliers start: 11 outliers final: 8 residues processed: 265 average time/residue: 0.3105 time to fit residues: 112.4402 Evaluate side-chains 236 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 228 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain A residue 955 LYS Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 979 ARG Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain M residue 936 LYS Chi-restraints excluded: chain M residue 947 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 30.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 73 ASN K 68 GLN L 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.084598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.051559 restraints weight = 47552.300| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.58 r_work: 0.2655 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2650 r_free = 0.2650 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14963 Z= 0.156 Angle : 0.616 22.987 21474 Z= 0.342 Chirality : 0.036 0.151 2432 Planarity : 0.004 0.046 1710 Dihedral : 29.317 169.594 4379 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.04 % Allowed : 8.77 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.04 (0.27), residues: 1008 helix: 2.26 (0.21), residues: 644 sheet: -0.18 (0.81), residues: 39 loop : -0.29 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 36 HIS 0.005 0.001 HIS F 75 PHE 0.024 0.001 PHE R 13 TYR 0.017 0.002 TYR H 83 ARG 0.015 0.001 ARG A 981 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 844) hydrogen bonds : angle 3.07204 ( 2146) metal coordination : bond 0.01310 ( 14) metal coordination : angle 10.17440 ( 9) covalent geometry : bond 0.00338 (14947) covalent geometry : angle 0.57934 (21465) Misc. bond : bond 0.00191 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 262 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9640 (mt) cc_final: 0.9403 (tt) REVERT: C 73 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8678 (t0) REVERT: C 90 ASP cc_start: 0.8849 (t70) cc_final: 0.8592 (t70) REVERT: D 68 ASP cc_start: 0.9385 (t70) cc_final: 0.9119 (t0) REVERT: D 93 GLU cc_start: 0.9168 (mp0) cc_final: 0.8566 (mp0) REVERT: E 56 LYS cc_start: 0.9344 (ttmt) cc_final: 0.9096 (ttmm) REVERT: E 59 GLU cc_start: 0.9130 (pm20) cc_final: 0.8913 (pm20) REVERT: G 13 LYS cc_start: 0.7375 (tptt) cc_final: 0.7172 (tppt) REVERT: G 36 LYS cc_start: 0.8879 (tmtt) cc_final: 0.8638 (tmtt) REVERT: G 90 ASP cc_start: 0.8649 (t70) cc_final: 0.8269 (t0) REVERT: K 56 LYS cc_start: 0.9364 (ttmm) cc_final: 0.9126 (ttpp) REVERT: K 59 GLU cc_start: 0.8849 (pm20) cc_final: 0.8443 (pm20) REVERT: A 970 GLU cc_start: 0.9434 (pm20) cc_final: 0.9117 (pm20) REVERT: M 926 ASN cc_start: 0.9193 (m110) cc_final: 0.8930 (m110) REVERT: M 938 PHE cc_start: 0.9166 (m-80) cc_final: 0.8459 (m-80) REVERT: M 951 ASP cc_start: 0.9215 (m-30) cc_final: 0.8731 (p0) REVERT: M 967 ASN cc_start: 0.9266 (m-40) cc_final: 0.8776 (m-40) REVERT: R 80 ASN cc_start: 0.8280 (t0) cc_final: 0.7377 (t0) outliers start: 17 outliers final: 8 residues processed: 268 average time/residue: 0.3134 time to fit residues: 115.0749 Evaluate side-chains 247 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 238 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain K residue 51 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 936 LYS Chi-restraints excluded: chain R residue 89 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 114 optimal weight: 40.0000 chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN G 73 ASN K 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.084059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.051063 restraints weight = 47636.851| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.58 r_work: 0.2641 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2636 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2636 r_free = 0.2636 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2636 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14963 Z= 0.176 Angle : 0.612 18.189 21474 Z= 0.344 Chirality : 0.036 0.161 2432 Planarity : 0.004 0.060 1710 Dihedral : 29.277 169.780 4361 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.32 % Allowed : 13.10 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.09 (0.26), residues: 1008 helix: 2.32 (0.21), residues: 644 sheet: 0.14 (0.86), residues: 39 loop : -0.37 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 36 HIS 0.012 0.001 HIS A 996 PHE 0.014 0.001 PHE M 938 TYR 0.037 0.002 TYR H 83 ARG 0.008 0.000 ARG A 979 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 844) hydrogen bonds : angle 3.03011 ( 2146) metal coordination : bond 0.00971 ( 14) metal coordination : angle 9.38801 ( 9) covalent geometry : bond 0.00390 (14947) covalent geometry : angle 0.58142 (21465) Misc. bond : bond 0.00354 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 247 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9652 (mt) cc_final: 0.9423 (tt) REVERT: C 90 ASP cc_start: 0.8882 (t70) cc_final: 0.8577 (t70) REVERT: D 68 ASP cc_start: 0.9391 (t70) cc_final: 0.9138 (t0) REVERT: E 59 GLU cc_start: 0.9108 (pm20) cc_final: 0.8871 (pm20) REVERT: F 88 TYR cc_start: 0.9212 (m-10) cc_final: 0.8880 (m-10) REVERT: G 73 ASN cc_start: 0.8757 (t160) cc_final: 0.8273 (t0) REVERT: G 90 ASP cc_start: 0.8575 (t70) cc_final: 0.8168 (t0) REVERT: H 46 LYS cc_start: 0.9235 (mmmt) cc_final: 0.8938 (mmmt) REVERT: K 56 LYS cc_start: 0.9394 (ttmm) cc_final: 0.9153 (ttpp) REVERT: K 59 GLU cc_start: 0.8854 (pm20) cc_final: 0.8426 (pm20) REVERT: A 996 HIS cc_start: 0.6753 (t-170) cc_final: 0.6549 (t-170) REVERT: M 938 PHE cc_start: 0.9223 (m-80) cc_final: 0.8714 (m-80) REVERT: M 951 ASP cc_start: 0.9185 (m-30) cc_final: 0.8748 (p0) REVERT: M 967 ASN cc_start: 0.9211 (m-40) cc_final: 0.8698 (m-40) outliers start: 11 outliers final: 6 residues processed: 255 average time/residue: 0.2985 time to fit residues: 105.0223 Evaluate side-chains 242 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 236 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain M residue 920 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 14 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN K 68 GLN R 80 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.083519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.050547 restraints weight = 47503.161| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.56 r_work: 0.2629 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2624 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2624 r_free = 0.2624 target_work(ls_wunit_k1) = 0.041 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2624 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14963 Z= 0.193 Angle : 0.605 15.047 21474 Z= 0.342 Chirality : 0.037 0.163 2432 Planarity : 0.004 0.037 1710 Dihedral : 29.315 169.213 4357 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.56 % Allowed : 13.82 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.08 (0.26), residues: 1008 helix: 2.32 (0.20), residues: 644 sheet: 0.50 (0.90), residues: 39 loop : -0.44 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 36 HIS 0.006 0.001 HIS F 75 PHE 0.012 0.001 PHE M 938 TYR 0.057 0.002 TYR H 83 ARG 0.007 0.000 ARG A 981 Details of bonding type rmsd hydrogen bonds : bond 0.03999 ( 844) hydrogen bonds : angle 3.00892 ( 2146) metal coordination : bond 0.00836 ( 14) metal coordination : angle 8.39258 ( 9) covalent geometry : bond 0.00434 (14947) covalent geometry : angle 0.58009 (21465) Misc. bond : bond 0.00115 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 242 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9650 (mt) cc_final: 0.9417 (tt) REVERT: C 90 ASP cc_start: 0.8937 (t70) cc_final: 0.8616 (t70) REVERT: D 68 ASP cc_start: 0.9403 (t70) cc_final: 0.9156 (t0) REVERT: E 59 GLU cc_start: 0.9113 (pm20) cc_final: 0.8861 (pm20) REVERT: G 73 ASN cc_start: 0.8816 (t160) cc_final: 0.8270 (t0) REVERT: G 90 ASP cc_start: 0.8658 (t70) cc_final: 0.8240 (t0) REVERT: H 46 LYS cc_start: 0.9264 (mmmt) cc_final: 0.9025 (mmmt) REVERT: K 56 LYS cc_start: 0.9395 (ttmm) cc_final: 0.9150 (ttpp) REVERT: K 59 GLU cc_start: 0.8847 (pm20) cc_final: 0.8416 (pm20) REVERT: M 938 PHE cc_start: 0.9198 (m-80) cc_final: 0.8567 (m-80) REVERT: M 951 ASP cc_start: 0.9187 (m-30) cc_final: 0.8711 (p0) REVERT: M 967 ASN cc_start: 0.9195 (m-40) cc_final: 0.8913 (m-40) REVERT: R 15 ARG cc_start: 0.7901 (mtm-85) cc_final: 0.7639 (mtm110) outliers start: 13 outliers final: 10 residues processed: 253 average time/residue: 0.2948 time to fit residues: 103.5891 Evaluate side-chains 243 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 233 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain M residue 920 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 0.0980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 0.0670 chunk 44 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.084653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051826 restraints weight = 47897.096| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 2.59 r_work: 0.2662 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14963 Z= 0.151 Angle : 0.602 19.808 21474 Z= 0.337 Chirality : 0.036 0.173 2432 Planarity : 0.004 0.094 1710 Dihedral : 29.244 168.652 4357 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.80 % Allowed : 15.50 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 2.17 (0.27), residues: 1008 helix: 2.39 (0.20), residues: 644 sheet: 0.97 (0.95), residues: 39 loop : -0.47 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 36 HIS 0.017 0.001 HIS A 996 PHE 0.013 0.001 PHE R 13 TYR 0.043 0.002 TYR D 83 ARG 0.012 0.000 ARG A 979 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 844) hydrogen bonds : angle 2.90970 ( 2146) metal coordination : bond 0.00547 ( 14) metal coordination : angle 9.46962 ( 9) covalent geometry : bond 0.00327 (14947) covalent geometry : angle 0.56982 (21465) Misc. bond : bond 0.00310 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 257 time to evaluate : 1.089 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: C 90 ASP cc_start: 0.8881 (t70) cc_final: 0.8589 (t70) REVERT: D 68 ASP cc_start: 0.9401 (t70) cc_final: 0.9121 (t0) REVERT: E 59 GLU cc_start: 0.9100 (pm20) cc_final: 0.8842 (pm20) REVERT: E 120 MET cc_start: 0.8586 (mtp) cc_final: 0.8298 (mtp) REVERT: G 73 ASN cc_start: 0.8823 (t160) cc_final: 0.8564 (t0) REVERT: H 46 LYS cc_start: 0.9263 (mmmt) cc_final: 0.9000 (mmmt) REVERT: H 83 TYR cc_start: 0.7402 (m-80) cc_final: 0.6891 (m-80) REVERT: H 93 GLU cc_start: 0.8810 (mp0) cc_final: 0.8601 (mp0) REVERT: K 56 LYS cc_start: 0.9375 (ttmm) cc_final: 0.9128 (ttpp) REVERT: K 59 GLU cc_start: 0.8816 (pm20) cc_final: 0.8432 (pm20) REVERT: A 969 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 996 HIS cc_start: 0.6504 (t-170) cc_final: 0.6074 (t-170) REVERT: M 938 PHE cc_start: 0.9246 (m-80) cc_final: 0.8752 (m-80) REVERT: M 951 ASP cc_start: 0.9160 (m-30) cc_final: 0.8681 (p0) REVERT: M 955 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7152 (mtm-85) REVERT: M 967 ASN cc_start: 0.9205 (m-40) cc_final: 0.8785 (m-40) REVERT: M 968 ASP cc_start: 0.9302 (m-30) cc_final: 0.8353 (t0) outliers start: 15 outliers final: 11 residues processed: 264 average time/residue: 0.2981 time to fit residues: 109.3525 Evaluate side-chains 252 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 240 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain M residue 920 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.7424 > 50: distance: 11 - 38: 16.938 distance: 18 - 49: 28.490 distance: 28 - 32: 9.797 distance: 32 - 33: 7.051 distance: 33 - 34: 10.337 distance: 33 - 36: 11.866 distance: 34 - 35: 18.645 distance: 34 - 38: 5.303 distance: 36 - 37: 24.296 distance: 38 - 39: 15.906 distance: 39 - 40: 13.229 distance: 39 - 42: 24.797 distance: 40 - 41: 43.283 distance: 40 - 49: 3.881 distance: 42 - 43: 19.094 distance: 43 - 44: 24.779 distance: 44 - 45: 11.193 distance: 45 - 46: 6.892 distance: 46 - 47: 12.683 distance: 46 - 48: 13.535 distance: 49 - 50: 7.872 distance: 50 - 51: 27.125 distance: 50 - 53: 12.603 distance: 51 - 52: 53.053 distance: 51 - 54: 28.351 distance: 54 - 55: 52.191 distance: 56 - 58: 23.409 distance: 58 - 59: 17.134 distance: 59 - 60: 12.423 distance: 59 - 62: 38.951 distance: 60 - 61: 19.235 distance: 60 - 66: 26.087 distance: 62 - 63: 28.030 distance: 63 - 64: 35.619 distance: 63 - 65: 10.043 distance: 66 - 67: 29.047 distance: 67 - 68: 42.362 distance: 67 - 70: 11.271 distance: 68 - 69: 42.618 distance: 68 - 75: 6.987 distance: 70 - 71: 41.875 distance: 71 - 72: 34.424 distance: 72 - 73: 40.808 distance: 72 - 74: 47.288 distance: 75 - 76: 41.294 distance: 76 - 77: 33.897 distance: 76 - 79: 23.068 distance: 77 - 78: 9.588 distance: 77 - 86: 16.868 distance: 79 - 80: 20.428 distance: 80 - 81: 23.793 distance: 80 - 82: 18.838 distance: 81 - 83: 23.632 distance: 82 - 84: 29.376 distance: 83 - 85: 23.055 distance: 84 - 85: 26.097 distance: 86 - 87: 18.509 distance: 86 - 92: 45.585 distance: 87 - 88: 36.482 distance: 87 - 90: 18.720 distance: 88 - 89: 27.948 distance: 88 - 93: 16.587 distance: 89 - 113: 16.845 distance: 90 - 91: 46.190 distance: 91 - 92: 24.188 distance: 93 - 94: 6.910 distance: 94 - 95: 19.858 distance: 94 - 97: 13.045 distance: 95 - 96: 7.743 distance: 95 - 100: 11.650 distance: 96 - 120: 11.287 distance: 97 - 98: 12.845 distance: 97 - 99: 19.008 distance: 100 - 101: 17.581 distance: 101 - 102: 20.584 distance: 102 - 103: 9.963 distance: 102 - 104: 19.381 distance: 103 - 126: 18.429