Starting phenix.real_space_refine on Sat Mar 16 16:23:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iej_35383/03_2024/8iej_35383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iej_35383/03_2024/8iej_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iej_35383/03_2024/8iej_35383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iej_35383/03_2024/8iej_35383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iej_35383/03_2024/8iej_35383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iej_35383/03_2024/8iej_35383.pdb" } 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 Residue "C GLU 41": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H ASP 68": "OD1" <-> "OD2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "K ASP 77": "OD1" <-> "OD2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "A PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 979": "NH1" <-> "NH2" Residue "A ARG 981": "NH1" <-> "NH2" Residue "A TYR 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 941": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 964": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 973": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 140": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.75, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 1.7 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: 6.38 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: 5.41 Time building geometry restraints manager: 7.48 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: 95.05 - 102.86: 458 102.86 - 110.67: 6558 110.67 - 118.48: 5935 118.48 - 126.29: 7582 126.29 - 134.09: 932 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: 7 2.12 - 2.81: 3441 2.81 - 3.51: 20076 3.51 - 4.20: 39166 4.20 - 4.90: 58629 Nonbonded interactions: 121319 Sorted by model distance: nonbonded pdb=" OH TYR A 999 " pdb=" NE2 HIS M 939 " model vdw 1.421 2.520 nonbonded pdb=" OH TYR A 999 " pdb=" CD2 HIS M 939 " model vdw 1.627 3.260 nonbonded pdb=" NH1 ARG A 979 " pdb=" CZ ARG A 981 " model vdw 1.646 3.350 nonbonded pdb=" NH1 ARG A 997 " pdb=" CD1 TYR A 999 " model vdw 1.787 3.420 nonbonded pdb=" NH1 ARG A 979 " pdb=" NH1 ARG A 981 " model vdw 1.960 3.200 ... (remaining 121314 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.290 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 47.580 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.510 ------------------------------------------------------------------------------- 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 : 0.006 0.052 14947 Z= 0.316 Angle : 0.638 13.124 21465 Z= 0.382 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 *********************** 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 fitting. rotamer outliers: 11 poor density : 256 time to evaluate : 1.372 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: 0.3142 time to fit residues: 113.3787 Evaluate side-chains 236 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 228 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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: 3.9990 chunk 95 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 114 optimal weight: 30.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 104 GLN G 73 ASN K 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14947 Z= 0.246 Angle : 0.580 6.717 21465 Z= 0.342 Chirality : 0.037 0.155 2432 Planarity : 0.004 0.036 1710 Dihedral : 29.400 169.624 4379 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.16 % Allowed : 10.10 % Favored : 87.74 % 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: 2.11 (0.27), residues: 1008 helix: 2.31 (0.21), residues: 645 sheet: -0.18 (0.79), residues: 39 loop : -0.25 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 36 HIS 0.006 0.001 HIS F 75 PHE 0.030 0.002 PHE R 13 TYR 0.019 0.002 TYR A 976 ARG 0.009 0.000 ARG A 997 *********************** 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 268 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 250 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 ILE cc_start: 0.9578 (mt) cc_final: 0.9368 (tt) REVERT: C 73 ASN cc_start: 0.9019 (OUTLIER) cc_final: 0.8558 (t0) REVERT: C 90 ASP cc_start: 0.8511 (t70) cc_final: 0.8261 (t70) REVERT: D 68 ASP cc_start: 0.8886 (t70) cc_final: 0.8661 (t0) REVERT: D 108 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8700 (ttpp) REVERT: F 88 TYR cc_start: 0.9067 (m-10) cc_final: 0.8404 (m-10) REVERT: G 13 LYS cc_start: 0.7325 (tptt) cc_final: 0.6789 (tppt) REVERT: G 36 LYS cc_start: 0.8706 (tmtt) cc_final: 0.8428 (tmtt) REVERT: G 90 ASP cc_start: 0.8490 (t70) cc_final: 0.8178 (t0) REVERT: K 56 LYS cc_start: 0.9342 (ttmm) cc_final: 0.9113 (ttpp) REVERT: K 59 GLU cc_start: 0.8663 (pm20) cc_final: 0.8328 (pm20) REVERT: A 997 ARG cc_start: 0.8273 (tmm160) cc_final: 0.7986 (ttp80) REVERT: M 938 PHE cc_start: 0.9038 (m-80) cc_final: 0.8423 (m-80) REVERT: M 951 ASP cc_start: 0.8963 (m-30) cc_final: 0.8569 (p0) REVERT: M 967 ASN cc_start: 0.9270 (m-40) cc_final: 0.8807 (m-40) outliers start: 18 outliers final: 9 residues processed: 257 average time/residue: 0.3172 time to fit residues: 110.9423 Evaluate side-chains 245 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 234 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 999 TYR 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 63 optimal weight: 4.9990 chunk 35 optimal weight: 30.0000 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 102 optimal weight: 8.9990 chunk 113 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN K 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14947 Z= 0.308 Angle : 0.601 7.683 21465 Z= 0.353 Chirality : 0.038 0.170 2432 Planarity : 0.004 0.042 1710 Dihedral : 29.420 169.260 4367 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.04 % Allowed : 12.86 % Favored : 85.10 % 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: 2.11 (0.27), residues: 1008 helix: 2.32 (0.21), residues: 644 sheet: 0.10 (0.88), residues: 39 loop : -0.33 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 36 HIS 0.011 0.001 HIS A 996 PHE 0.014 0.002 PHE R 13 TYR 0.042 0.002 TYR H 83 ARG 0.007 0.000 ARG A 973 *********************** 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 259 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 242 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8596 (t70) cc_final: 0.8311 (t70) REVERT: D 68 ASP cc_start: 0.8906 (t70) cc_final: 0.8686 (t0) REVERT: G 90 ASP cc_start: 0.8485 (t70) cc_final: 0.8145 (t0) REVERT: H 93 GLU cc_start: 0.8450 (mp0) cc_final: 0.8138 (mp0) REVERT: K 56 LYS cc_start: 0.9353 (ttmm) cc_final: 0.9115 (ttpp) REVERT: K 59 GLU cc_start: 0.8676 (pm20) cc_final: 0.8346 (pm20) REVERT: K 81 ASP cc_start: 0.8446 (m-30) cc_final: 0.8233 (m-30) REVERT: A 997 ARG cc_start: 0.8491 (tmm160) cc_final: 0.8202 (ttp80) REVERT: M 938 PHE cc_start: 0.9089 (m-80) cc_final: 0.8610 (m-80) REVERT: M 967 ASN cc_start: 0.9182 (m-40) cc_final: 0.8739 (m-40) REVERT: M 968 ASP cc_start: 0.9301 (m-30) cc_final: 0.9088 (m-30) REVERT: R 12 ASP cc_start: 0.8531 (m-30) cc_final: 0.8100 (m-30) REVERT: R 15 ARG cc_start: 0.7369 (mtm-85) cc_final: 0.7044 (mtt90) outliers start: 17 outliers final: 11 residues processed: 249 average time/residue: 0.3091 time to fit residues: 105.1518 Evaluate side-chains 238 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 227 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 87 ILE 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 H residue 51 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 971 CYS Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain R residue 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 0.0870 chunk 121 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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 L 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14947 Z= 0.245 Angle : 0.581 7.643 21465 Z= 0.342 Chirality : 0.037 0.192 2432 Planarity : 0.004 0.037 1710 Dihedral : 29.397 168.466 4359 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.68 % Allowed : 14.42 % Favored : 83.89 % 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: 2.24 (0.27), residues: 1008 helix: 2.42 (0.21), residues: 645 sheet: 0.35 (0.91), residues: 39 loop : -0.29 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 36 HIS 0.014 0.001 HIS A 996 PHE 0.011 0.001 PHE M 938 TYR 0.053 0.002 TYR H 83 ARG 0.006 0.000 ARG R 11 *********************** 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 259 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 245 time to evaluate : 1.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8597 (t70) cc_final: 0.8286 (t70) REVERT: D 68 ASP cc_start: 0.8905 (t70) cc_final: 0.8672 (t0) REVERT: G 73 ASN cc_start: 0.8570 (t160) cc_final: 0.8091 (t0) REVERT: G 90 ASP cc_start: 0.8433 (t70) cc_final: 0.8055 (t0) REVERT: H 93 GLU cc_start: 0.8445 (mp0) cc_final: 0.8176 (mp0) REVERT: K 56 LYS cc_start: 0.9344 (ttmm) cc_final: 0.9107 (ttpp) REVERT: K 59 GLU cc_start: 0.8721 (pm20) cc_final: 0.8370 (pm20) REVERT: M 938 PHE cc_start: 0.9148 (m-80) cc_final: 0.8714 (m-80) REVERT: M 967 ASN cc_start: 0.9114 (m-40) cc_final: 0.8795 (m-40) REVERT: M 968 ASP cc_start: 0.9297 (m-30) cc_final: 0.9036 (m-30) outliers start: 14 outliers final: 12 residues processed: 254 average time/residue: 0.3072 time to fit residues: 106.4316 Evaluate side-chains 247 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 235 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU 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 50 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 51 ASP 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 999 TYR 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 101 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 84 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14947 Z= 0.192 Angle : 0.566 7.513 21465 Z= 0.333 Chirality : 0.035 0.154 2432 Planarity : 0.004 0.038 1710 Dihedral : 29.319 168.163 4359 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.28 % Allowed : 15.14 % Favored : 82.57 % 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: 2.35 (0.27), residues: 1008 helix: 2.50 (0.21), residues: 645 sheet: 0.89 (1.07), residues: 29 loop : -0.28 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 36 HIS 0.006 0.001 HIS A 996 PHE 0.013 0.001 PHE A 964 TYR 0.042 0.002 TYR H 83 ARG 0.007 0.000 ARG R 11 *********************** 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 267 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 248 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8565 (t70) cc_final: 0.8289 (t0) REVERT: C 92 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8288 (mm-30) REVERT: D 68 ASP cc_start: 0.8900 (t70) cc_final: 0.8657 (t0) REVERT: G 73 ASN cc_start: 0.8569 (t160) cc_final: 0.8342 (t0) REVERT: H 93 GLU cc_start: 0.8389 (mp0) cc_final: 0.8124 (mp0) REVERT: K 56 LYS cc_start: 0.9343 (ttmm) cc_final: 0.9093 (ttpp) REVERT: K 59 GLU cc_start: 0.8714 (pm20) cc_final: 0.8370 (pm20) REVERT: A 950 CYS cc_start: 0.7775 (OUTLIER) cc_final: 0.6762 (p) REVERT: A 969 PHE cc_start: 0.8258 (OUTLIER) cc_final: 0.7955 (m-80) REVERT: A 996 HIS cc_start: 0.6625 (t-170) cc_final: 0.6183 (t-170) REVERT: A 997 ARG cc_start: 0.8418 (ttp80) cc_final: 0.7763 (ttp80) REVERT: M 938 PHE cc_start: 0.9122 (m-80) cc_final: 0.8492 (m-80) REVERT: M 967 ASN cc_start: 0.9105 (m-40) cc_final: 0.8705 (m-40) REVERT: M 968 ASP cc_start: 0.9259 (m-30) cc_final: 0.9009 (m-30) outliers start: 19 outliers final: 13 residues processed: 259 average time/residue: 0.2879 time to fit residues: 103.6580 Evaluate side-chains 252 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 237 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 108 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 H residue 51 ASP Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 950 CYS Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain M residue 920 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 0.0170 chunk 121 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 56 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN C 73 ASN H 84 ASN K 68 GLN M 926 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 14947 Z= 0.453 Angle : 0.665 7.732 21465 Z= 0.386 Chirality : 0.043 0.166 2432 Planarity : 0.005 0.070 1710 Dihedral : 29.772 167.630 4358 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.88 % Allowed : 16.11 % Favored : 81.01 % 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: 1.92 (0.27), residues: 1008 helix: 2.13 (0.21), residues: 647 sheet: 0.34 (0.92), residues: 37 loop : -0.36 (0.34), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP R 36 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.002 PHE M 938 TYR 0.070 0.003 TYR H 83 ARG 0.004 0.001 ARG M 928 *********************** REFINEMENT MACRO_CYCLE 6 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 256 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 232 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8645 (t70) cc_final: 0.8325 (t0) REVERT: D 83 TYR cc_start: 0.7393 (m-10) cc_final: 0.6830 (m-10) REVERT: G 73 ASN cc_start: 0.8916 (t160) cc_final: 0.8594 (t0) REVERT: G 90 ASP cc_start: 0.8563 (t70) cc_final: 0.8269 (t0) REVERT: H 93 GLU cc_start: 0.8642 (mp0) cc_final: 0.8415 (mp0) REVERT: K 56 LYS cc_start: 0.9379 (ttmm) cc_final: 0.9113 (ttpp) REVERT: K 59 GLU cc_start: 0.8769 (pm20) cc_final: 0.8319 (pm20) REVERT: L 88 TYR cc_start: 0.8877 (m-10) cc_final: 0.8487 (m-10) REVERT: A 950 CYS cc_start: 0.7958 (OUTLIER) cc_final: 0.6977 (p) REVERT: A 969 PHE cc_start: 0.8303 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 997 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7801 (ttp80) REVERT: M 938 PHE cc_start: 0.9065 (m-80) cc_final: 0.8426 (m-80) REVERT: M 968 ASP cc_start: 0.9269 (m-30) cc_final: 0.9028 (m-30) REVERT: R 36 TRP cc_start: 0.7692 (m100) cc_final: 0.7274 (m100) outliers start: 24 outliers final: 16 residues processed: 247 average time/residue: 0.3092 time to fit residues: 104.5557 Evaluate side-chains 238 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 220 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 120 CYS Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 950 CYS Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 995 PHE Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain R residue 16 LEU Chi-restraints excluded: chain R residue 87 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14947 Z= 0.313 Angle : 0.618 8.150 21465 Z= 0.361 Chirality : 0.039 0.165 2432 Planarity : 0.004 0.037 1710 Dihedral : 29.627 166.274 4358 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.76 % Allowed : 17.55 % Favored : 79.69 % 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: 2.02 (0.27), residues: 1008 helix: 2.27 (0.21), residues: 645 sheet: 0.08 (0.89), residues: 37 loop : -0.41 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 36 HIS 0.022 0.002 HIS A 996 PHE 0.015 0.002 PHE M 938 TYR 0.077 0.002 TYR H 83 ARG 0.005 0.000 ARG R 11 *********************** REFINEMENT MACRO_CYCLE 7 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 257 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 234 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8663 (t70) cc_final: 0.8344 (t0) REVERT: G 73 ASN cc_start: 0.8929 (t160) cc_final: 0.8568 (t0) REVERT: G 90 ASP cc_start: 0.8490 (t70) cc_final: 0.8165 (t0) REVERT: H 93 GLU cc_start: 0.8604 (mp0) cc_final: 0.8319 (mp0) REVERT: K 56 LYS cc_start: 0.9366 (ttmm) cc_final: 0.9112 (ttpp) REVERT: K 59 GLU cc_start: 0.8855 (pm20) cc_final: 0.8428 (pm20) REVERT: A 950 CYS cc_start: 0.7878 (OUTLIER) cc_final: 0.6930 (p) REVERT: A 969 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: M 938 PHE cc_start: 0.9146 (m-80) cc_final: 0.8654 (m-80) REVERT: M 968 ASP cc_start: 0.9236 (m-30) cc_final: 0.8977 (m-30) REVERT: R 36 TRP cc_start: 0.7641 (m100) cc_final: 0.7185 (m100) outliers start: 23 outliers final: 18 residues processed: 248 average time/residue: 0.2972 time to fit residues: 101.0117 Evaluate side-chains 244 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 224 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU 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 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 950 CYS Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 946 VAL Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 62 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14947 Z= 0.258 Angle : 0.612 8.049 21465 Z= 0.358 Chirality : 0.038 0.166 2432 Planarity : 0.004 0.037 1710 Dihedral : 29.560 166.181 4358 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.88 % Allowed : 17.31 % Favored : 79.81 % 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: 2.07 (0.27), residues: 1008 helix: 2.34 (0.21), residues: 645 sheet: -0.06 (0.85), residues: 37 loop : -0.45 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 36 HIS 0.018 0.001 HIS A 996 PHE 0.013 0.002 PHE M 938 TYR 0.055 0.002 TYR H 83 ARG 0.006 0.000 ARG R 11 *********************** REFINEMENT MACRO_CYCLE 8 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 253 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8681 (t70) cc_final: 0.8334 (t0) REVERT: G 73 ASN cc_start: 0.8917 (t160) cc_final: 0.8561 (t0) REVERT: G 90 ASP cc_start: 0.8477 (t70) cc_final: 0.8003 (t0) REVERT: H 93 GLU cc_start: 0.8565 (mp0) cc_final: 0.8279 (mp0) REVERT: K 56 LYS cc_start: 0.9359 (ttmm) cc_final: 0.9111 (ttpp) REVERT: K 59 GLU cc_start: 0.8843 (pm20) cc_final: 0.8411 (pm20) REVERT: A 950 CYS cc_start: 0.7804 (OUTLIER) cc_final: 0.6810 (p) REVERT: A 969 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: M 938 PHE cc_start: 0.9124 (m-80) cc_final: 0.8577 (m-80) REVERT: M 968 ASP cc_start: 0.9249 (m-30) cc_final: 0.8970 (m-30) REVERT: R 36 TRP cc_start: 0.7632 (m100) cc_final: 0.7137 (m100) outliers start: 24 outliers final: 18 residues processed: 241 average time/residue: 0.3012 time to fit residues: 100.1622 Evaluate side-chains 246 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 226 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 950 CYS Chi-restraints excluded: chain A residue 969 PHE 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 A residue 999 TYR Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 933 VAL Chi-restraints excluded: chain M residue 946 VAL Chi-restraints excluded: chain R residue 13 PHE Chi-restraints excluded: chain R residue 62 GLU Chi-restraints excluded: chain R residue 72 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 8.9990 chunk 116 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14947 Z= 0.256 Angle : 0.615 9.001 21465 Z= 0.359 Chirality : 0.037 0.165 2432 Planarity : 0.004 0.037 1710 Dihedral : 29.509 166.050 4357 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.64 % Allowed : 17.91 % Favored : 79.45 % 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: 2.10 (0.27), residues: 1008 helix: 2.33 (0.21), residues: 645 sheet: 0.74 (0.97), residues: 27 loop : -0.44 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 36 HIS 0.015 0.001 HIS A 996 PHE 0.014 0.002 PHE M 941 TYR 0.050 0.002 TYR H 83 ARG 0.004 0.000 ARG M 955 *********************** REFINEMENT MACRO_CYCLE 9 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 fitting. rotamer outliers: 22 poor density : 233 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9048 (t0) cc_final: 0.8755 (t0) REVERT: C 90 ASP cc_start: 0.8668 (t70) cc_final: 0.8313 (t0) REVERT: C 92 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8160 (mm-30) REVERT: C 95 LYS cc_start: 0.9449 (ttmt) cc_final: 0.9241 (ttmm) REVERT: G 73 ASN cc_start: 0.8895 (t160) cc_final: 0.8535 (t0) REVERT: G 90 ASP cc_start: 0.8464 (t70) cc_final: 0.7986 (t0) REVERT: H 93 GLU cc_start: 0.8563 (mp0) cc_final: 0.8274 (mp0) REVERT: K 56 LYS cc_start: 0.9368 (ttmm) cc_final: 0.9123 (ttpp) REVERT: K 59 GLU cc_start: 0.8840 (pm20) cc_final: 0.8406 (pm20) REVERT: A 950 CYS cc_start: 0.7819 (OUTLIER) cc_final: 0.6817 (p) REVERT: A 969 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: A 997 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8073 (ttp80) REVERT: A 999 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.7518 (p90) REVERT: M 938 PHE cc_start: 0.9112 (m-80) cc_final: 0.8483 (m-80) REVERT: M 968 ASP cc_start: 0.9238 (m-30) cc_final: 0.8939 (m-30) REVERT: R 36 TRP cc_start: 0.7624 (m100) cc_final: 0.7090 (m100) outliers start: 22 outliers final: 14 residues processed: 246 average time/residue: 0.3008 time to fit residues: 102.1449 Evaluate side-chains 243 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 950 CYS Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 969 PHE Chi-restraints excluded: chain A residue 983 CYS Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 TYR Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 933 VAL Chi-restraints excluded: chain R residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 83 optimal weight: 0.3980 chunk 125 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 30.0000 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14947 Z= 0.307 Angle : 0.640 8.727 21465 Z= 0.372 Chirality : 0.039 0.174 2432 Planarity : 0.004 0.037 1710 Dihedral : 29.573 165.722 4357 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.76 % Allowed : 18.63 % Favored : 78.61 % 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: 1.96 (0.27), residues: 1008 helix: 2.24 (0.21), residues: 646 sheet: -0.41 (0.83), residues: 38 loop : -0.42 (0.33), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 36 HIS 0.028 0.002 HIS A 996 PHE 0.019 0.002 PHE M 938 TYR 0.062 0.002 TYR H 83 ARG 0.005 0.000 ARG M 955 ********************** REFINEMENT MACRO_CYCLE 10 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 251 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 228 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.9104 (t0) cc_final: 0.8860 (t0) REVERT: C 90 ASP cc_start: 0.8702 (t70) cc_final: 0.8353 (t0) REVERT: C 95 LYS cc_start: 0.9454 (ttmt) cc_final: 0.9249 (ttmm) REVERT: G 73 ASN cc_start: 0.8927 (t160) cc_final: 0.8564 (t0) REVERT: G 90 ASP cc_start: 0.8497 (t70) cc_final: 0.8178 (t0) REVERT: H 93 GLU cc_start: 0.8591 (mp0) cc_final: 0.8305 (mp0) REVERT: K 56 LYS cc_start: 0.9369 (ttmm) cc_final: 0.9119 (ttpp) REVERT: K 59 GLU cc_start: 0.8820 (pm20) cc_final: 0.8359 (pm20) REVERT: K 81 ASP cc_start: 0.8416 (m-30) cc_final: 0.8210 (m-30) REVERT: A 950 CYS cc_start: 0.7836 (OUTLIER) cc_final: 0.6842 (p) REVERT: A 969 PHE cc_start: 0.8420 (OUTLIER) cc_final: 0.7783 (m-80) REVERT: M 938 PHE cc_start: 0.9135 (m-80) cc_final: 0.8544 (m-80) REVERT: M 968 ASP cc_start: 0.9211 (m-30) cc_final: 0.8925 (m-30) REVERT: R 36 TRP cc_start: 0.7602 (m100) cc_final: 0.7039 (m100) outliers start: 23 outliers final: 17 residues processed: 241 average time/residue: 0.2996 time to fit residues: 99.1202 Evaluate side-chains 247 residues out of total 873 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 228 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain L residue 77 LYS Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain A residue 950 CYS Chi-restraints excluded: chain A residue 962 LYS Chi-restraints excluded: chain A residue 969 PHE 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 A residue 999 TYR Chi-restraints excluded: chain M residue 920 LEU Chi-restraints excluded: chain M residue 933 VAL Chi-restraints excluded: chain M residue 946 VAL Chi-restraints excluded: chain R residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.083830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.050998 restraints weight = 47740.815| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.57 r_work: 0.2648 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 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 = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.042 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14947 Z= 0.187 Angle : 0.602 8.991 21465 Z= 0.351 Chirality : 0.036 0.157 2432 Planarity : 0.004 0.040 1710 Dihedral : 29.349 165.032 4357 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.80 % Allowed : 19.71 % Favored : 78.49 % 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: 2.10 (0.27), residues: 1008 helix: 2.37 (0.21), residues: 645 sheet: -0.22 (0.86), residues: 38 loop : -0.41 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 36 HIS 0.027 0.001 HIS A 996 PHE 0.015 0.001 PHE R 72 TYR 0.043 0.002 TYR H 83 ARG 0.004 0.000 ARG M 955 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3067.04 seconds wall clock time: 55 minutes 42.59 seconds (3342.59 seconds total)