Starting phenix.real_space_refine on Sun Jul 21 17:06:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp7_17797/07_2024/8pp7_17797_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp7_17797/07_2024/8pp7_17797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp7_17797/07_2024/8pp7_17797.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp7_17797/07_2024/8pp7_17797.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp7_17797/07_2024/8pp7_17797_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pp7_17797/07_2024/8pp7_17797_neut.cif" } resolution = 2.91 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= 0.003 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 304 5.49 5 S 52 5.16 5 C 8844 2.51 5 N 2879 2.21 5 O 3475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E GLU 97": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 15562 Number of models: 1 Model: "" Number of chains: 18 Chain: "K" Number of atoms: 846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 846 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "L" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 802 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 7, 'TRANS': 93} Chain: "M" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "N" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 793 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 7, 'TRANS': 92} Chain: "A" 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: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 812 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" 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: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 816 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 732 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "J" Number of atoms: 3152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3152 Classifications: {'DNA': 153} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 152} Chain: "I" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3116 Classifications: {'DNA': 153} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 152} Chain: "K" 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: "L" 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} Chain: "N" 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 132 SG CYS K 18 126.610 70.448 74.892 1.00 62.88 S ATOM 153 SG CYS K 21 129.967 68.919 75.715 1.00 61.18 S ATOM 291 SG CYS K 39 127.543 67.137 73.442 1.00 64.33 S ATOM 313 SG CYS K 42 126.862 67.333 77.232 1.00 62.33 S ATOM 250 SG CYS K 34 114.756 75.058 72.328 1.00 58.73 S ATOM 408 SG CYS K 53 116.923 75.195 75.485 1.00 61.76 S ATOM 429 SG CYS K 56 114.715 78.183 74.583 1.00 63.49 S ATOM 1144 SG CYS L 51 115.068 72.315 48.732 1.00 69.23 S ATOM 1165 SG CYS L 54 115.985 74.780 46.099 1.00 60.62 S ATOM 1313 SG CYS L 72 115.352 75.938 49.649 1.00 60.17 S ATOM 1332 SG CYS L 75 112.394 74.834 47.460 1.00 58.63 S ATOM 1267 SG CYS L 67 110.746 64.918 58.433 1.00 60.74 S ATOM 1421 SG CYS L 87 109.634 65.075 54.745 1.00 65.44 S ATOM 1441 SG CYS L 90 110.182 61.688 56.452 1.00 62.69 S ATOM 1780 SG CYS M 18 25.059 78.139 65.913 1.00 61.07 S ATOM 1801 SG CYS M 21 22.034 78.636 63.838 1.00 58.53 S ATOM 1939 SG CYS M 39 24.402 75.806 63.022 1.00 60.76 S ATOM 1961 SG CYS M 42 25.391 79.445 62.241 1.00 59.57 S ATOM 1898 SG CYS M 34 37.309 76.993 70.405 1.00 62.37 S ATOM 2056 SG CYS M 53 34.990 80.001 70.263 1.00 59.14 S ATOM 2077 SG CYS M 56 37.410 79.677 73.203 1.00 54.77 S ATOM 2754 SG CYS N 51 36.665 53.670 75.761 1.00 60.99 S ATOM 2775 SG CYS N 54 35.815 52.064 78.955 1.00 59.16 S ATOM 2923 SG CYS N 72 36.326 55.845 78.794 1.00 55.37 S ATOM 2942 SG CYS N 75 39.345 53.448 78.598 1.00 58.02 S ATOM 2877 SG CYS N 67 41.142 60.990 65.481 1.00 51.03 S ATOM 3031 SG CYS N 87 42.217 57.692 67.023 1.00 56.13 S ATOM 3051 SG CYS N 90 42.222 58.179 63.182 1.00 58.33 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LYS C 12 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 12 " occ=0.00 residue: pdb=" N GLY G 11 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 11 " occ=0.00 Time building chain proxies: 8.25, per 1000 atoms: 0.53 Number of scatterers: 15562 At special positions: 0 Unit cell: (153.85, 129.2, 126.65, 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 8 29.99 S 52 16.00 P 304 15.00 O 3475 8.00 N 2879 7.00 C 8844 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: 7.53 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 21 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 18 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 42 " pdb=" ZN K 402 " pdb="ZN ZN K 402 " - pdb=" ND1 HIS K 36 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 53 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 56 " pdb="ZN ZN K 402 " - pdb=" SG CYS K 34 " pdb=" ZN L 401 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 72 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 54 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 401 " - pdb=" SG CYS L 75 " pdb=" ZN L 402 " pdb="ZN ZN L 402 " - pdb=" ND1 HIS L 69 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 90 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 67 " pdb="ZN ZN L 402 " - pdb=" SG CYS L 87 " pdb=" ZN M 401 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 21 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 39 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 18 " pdb="ZN ZN M 401 " - pdb=" SG CYS M 42 " pdb=" ZN M 402 " pdb="ZN ZN M 402 " - pdb=" ND1 HIS M 36 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 53 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 56 " pdb="ZN ZN M 402 " - pdb=" SG CYS M 34 " pdb=" ZN N 401 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 54 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 51 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 72 " pdb="ZN ZN N 401 " - pdb=" SG CYS N 75 " pdb=" ZN N 402 " pdb="ZN ZN N 402 " - pdb=" ND1 HIS N 69 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 67 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 87 " pdb="ZN ZN N 402 " - pdb=" SG CYS N 90 " Number of angles added : 36 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2216 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 14 sheets defined 60.4% alpha, 5.2% beta 125 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 7.26 Creating SS restraints... Processing helix chain 'K' and resid 9 through 13 Processing helix chain 'K' and resid 14 through 17 removed outlier: 4.066A pdb=" N MET K 17 " --> pdb=" O PRO K 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 14 through 17' Processing helix chain 'K' and resid 40 through 50 removed outlier: 3.945A pdb=" N GLU K 48 " --> pdb=" O VAL K 44 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N THR K 49 " --> pdb=" O ARG K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 64 through 67 removed outlier: 3.540A pdb=" N LEU K 67 " --> pdb=" O ARG K 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 64 through 67' Processing helix chain 'K' and resid 72 through 83 Processing helix chain 'K' and resid 86 through 99 Processing helix chain 'L' and resid 73 through 82 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'L' and resid 103 through 114 removed outlier: 3.563A pdb=" N ASP L 107 " --> pdb=" O ASP L 103 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 13 Processing helix chain 'M' and resid 14 through 17 removed outlier: 3.787A pdb=" N MET M 17 " --> pdb=" O PRO M 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 14 through 17' Processing helix chain 'M' and resid 40 through 48 removed outlier: 3.769A pdb=" N GLU M 48 " --> pdb=" O VAL M 44 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 67 Processing helix chain 'M' and resid 72 through 83 Processing helix chain 'M' and resid 86 through 101 removed outlier: 3.691A pdb=" N HIS M 101 " --> pdb=" O PHE M 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 26 removed outlier: 3.722A pdb=" N ARG N 26 " --> pdb=" O GLU N 23 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 46 Processing helix chain 'N' and resid 73 through 82 Processing helix chain 'N' and resid 96 through 98 No H-bonds generated for 'chain 'N' and resid 96 through 98' Processing helix chain 'N' and resid 103 through 114 removed outlier: 3.552A pdb=" N ASP N 107 " --> pdb=" O ASP N 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.806A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.775A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.762A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.755A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 21 Processing helix chain 'C' and resid 25 through 35 removed outlier: 3.628A pdb=" N ILE C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 3.571A pdb=" N ASN C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 89 Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.884A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.578A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.585A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.643A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.481A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 15 through 21 Processing helix chain 'G' and resid 25 through 36 Processing helix chain 'G' and resid 45 through 72 Processing helix chain 'G' and resid 78 through 88 removed outlier: 3.512A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.506A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.777A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 5 through 8 removed outlier: 4.742A pdb=" N THR K 5 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N VAL L 40 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE K 7 " --> pdb=" O ILE L 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 36 through 39 Processing sheet with id=AA3, first strand: chain 'L' and resid 70 through 72 Processing sheet with id=AA4, first strand: chain 'M' and resid 5 through 8 removed outlier: 3.719A pdb=" N THR M 5 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL N 40 " --> pdb=" O THR M 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 37 through 39 Processing sheet with id=AA6, first strand: chain 'N' and resid 70 through 72 Processing sheet with id=AA7, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.931A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.991A pdb=" N THR B 96 " --> pdb=" O THR G 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.085A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.641A pdb=" N THR C 100 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.797A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'G' and resid 41 through 42 removed outlier: 7.200A pdb=" N ARG G 41 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'G' and resid 76 through 77 490 hydrogen bonds defined for protein. 1431 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 308 hydrogen bonds 616 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 5.55 Time building geometry restraints manager: 7.95 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: 3263 1.33 - 1.45: 4812 1.45 - 1.58: 7702 1.58 - 1.70: 608 1.70 - 1.82: 74 Bond restraints: 16459 Sorted by residual: bond pdb=" CG1 ILE B 26 " pdb=" CD1 ILE B 26 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.08e+00 bond pdb=" C ASN F 64 " pdb=" O ASN F 64 " ideal model delta sigma weight residual 1.236 1.248 -0.012 1.15e-02 7.56e+03 1.05e+00 bond pdb=" C1' DC J 52 " pdb=" N1 DC J 52 " ideal model delta sigma weight residual 1.490 1.519 -0.029 3.00e-02 1.11e+03 9.45e-01 bond pdb=" C2' DT I 91 " pdb=" C1' DT I 91 " ideal model delta sigma weight residual 1.525 1.506 0.019 2.00e-02 2.50e+03 9.07e-01 bond pdb=" C GLY A 102 " pdb=" O GLY A 102 " ideal model delta sigma weight residual 1.234 1.245 -0.011 1.20e-02 6.94e+03 9.03e-01 ... (remaining 16454 not shown) Histogram of bond angle deviations from ideal: 98.39 - 105.50: 1455 105.50 - 112.61: 9133 112.61 - 119.73: 5459 119.73 - 126.84: 6592 126.84 - 133.95: 899 Bond angle restraints: 23538 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.20 109.60 3.60 9.60e-01 1.09e+00 1.41e+01 angle pdb=" CB MET N 57 " pdb=" CG MET N 57 " pdb=" SD MET N 57 " ideal model delta sigma weight residual 112.70 120.21 -7.51 3.00e+00 1.11e-01 6.26e+00 angle pdb=" C3' DC J 7 " pdb=" C2' DC J 7 " pdb=" C1' DC J 7 " ideal model delta sigma weight residual 101.60 105.14 -3.54 1.50e+00 4.44e-01 5.56e+00 angle pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " pdb=" CG GLN E 76 " ideal model delta sigma weight residual 114.10 118.36 -4.26 2.00e+00 2.50e-01 4.53e+00 angle pdb=" C3' DA I -75 " pdb=" C2' DA I -75 " pdb=" C1' DA I -75 " ideal model delta sigma weight residual 101.60 104.76 -3.16 1.50e+00 4.44e-01 4.43e+00 ... (remaining 23533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6468 17.96 - 35.92: 1341 35.92 - 53.88: 1128 53.88 - 71.84: 256 71.84 - 89.79: 10 Dihedral angle restraints: 9203 sinusoidal: 5790 harmonic: 3413 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 162.57 17.43 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP M 57 " pdb=" CB ASP M 57 " pdb=" CG ASP M 57 " pdb=" OD1 ASP M 57 " ideal model delta sinusoidal sigma weight residual -30.00 -88.64 58.64 1 2.00e+01 2.50e-03 1.15e+01 dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 163.37 16.63 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 9200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1504 0.028 - 0.057: 791 0.057 - 0.085: 297 0.085 - 0.114: 70 0.114 - 0.142: 28 Chirality restraints: 2690 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE F 46 " pdb=" N ILE F 46 " pdb=" C ILE F 46 " pdb=" CB ILE F 46 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.86e-01 chirality pdb=" CA ILE M 26 " pdb=" N ILE M 26 " pdb=" C ILE M 26 " pdb=" CB ILE M 26 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2687 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO B 32 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J -12 " 0.021 2.00e-02 2.50e+03 9.55e-03 2.51e+00 pdb=" N9 DA J -12 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DA J -12 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA J -12 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA J -12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA J -12 " 0.000 2.00e-02 2.50e+03 pdb=" N6 DA J -12 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA J -12 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA J -12 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA J -12 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA J -12 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 93 " -0.020 2.00e-02 2.50e+03 9.30e-03 2.38e+00 pdb=" N9 DA I 93 " 0.022 2.00e-02 2.50e+03 pdb=" C8 DA I 93 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I 93 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 93 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 93 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 93 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 93 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 93 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 93 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA I 93 " 0.001 2.00e-02 2.50e+03 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1968 2.76 - 3.29: 13008 3.29 - 3.83: 26897 3.83 - 4.36: 33993 4.36 - 4.90: 49604 Nonbonded interactions: 125470 Sorted by model distance: nonbonded pdb=" OH TYR G 56 " pdb=" OE2 GLU G 60 " model vdw 2.222 2.440 nonbonded pdb=" O GLU K 33 " pdb=" NH1 ARG L 101 " model vdw 2.257 2.520 nonbonded pdb=" O SER H 120 " pdb=" OG SER H 120 " model vdw 2.325 2.440 nonbonded pdb=" N6 DA J -73 " pdb=" O6 DG I 148 " model vdw 2.329 2.520 nonbonded pdb=" OH TYR C 49 " pdb=" OE1 GLN D 92 " model vdw 2.336 2.440 ... (remaining 125465 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 117) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } ncs_group { reference = (chain 'K' and (resid 3 through 102 or resid 401 through 402)) selection = chain 'M' } ncs_group { reference = (chain 'L' and (resid 16 through 115 or resid 401 through 402)) selection = chain 'N' } 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=0.00 max=1.00 mean=0.98 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 50.330 Find NCS groups from input model: 0.820 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: 0.010 Load rotamer database and sin/cos tables:13.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 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 : 0.004 0.041 16459 Z= 0.255 Angle : 0.599 7.508 23538 Z= 0.360 Chirality : 0.039 0.142 2690 Planarity : 0.005 0.044 1909 Dihedral : 25.188 89.795 6987 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.69 % Allowed : 15.13 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.25), residues: 1141 helix: 1.85 (0.20), residues: 642 sheet: -0.40 (1.28), residues: 20 loop : -0.99 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP N 17 HIS 0.004 0.001 HIS C 30 PHE 0.012 0.001 PHE N 71 TYR 0.013 0.002 TYR H 34 ARG 0.006 0.001 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 180 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 0 residues processed: 185 average time/residue: 1.5687 time to fit residues: 313.9642 Evaluate side-chains 124 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 89 ASN L 29 GLN L 69 HIS B 25 ASN C 103 GLN E 76 GLN G 88 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16459 Z= 0.313 Angle : 0.596 7.534 23538 Z= 0.347 Chirality : 0.038 0.179 2690 Planarity : 0.004 0.037 1909 Dihedral : 28.440 77.887 4630 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.77 % Allowed : 16.12 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.37 (0.25), residues: 1141 helix: 2.15 (0.21), residues: 653 sheet: -0.06 (1.54), residues: 15 loop : -0.89 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 17 HIS 0.002 0.001 HIS H 106 PHE 0.020 0.002 PHE M 38 TYR 0.009 0.001 TYR C 49 ARG 0.010 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6679 (mm) outliers start: 28 outliers final: 5 residues processed: 147 average time/residue: 1.6824 time to fit residues: 266.8749 Evaluate side-chains 121 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 115 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain H residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 6.9990 chunk 40 optimal weight: 6.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 35 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 128 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 103 optimal weight: 0.0370 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 89 ASN B 75 HIS C 103 GLN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 16459 Z= 0.338 Angle : 0.582 8.033 23538 Z= 0.340 Chirality : 0.038 0.170 2690 Planarity : 0.004 0.038 1909 Dihedral : 28.340 76.237 4630 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.57 % Allowed : 17.90 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.25), residues: 1141 helix: 2.17 (0.21), residues: 653 sheet: 0.05 (1.53), residues: 15 loop : -0.91 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 17 HIS 0.020 0.001 HIS L 69 PHE 0.014 0.002 PHE H 62 TYR 0.009 0.001 TYR C 49 ARG 0.008 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7257 (OUTLIER) cc_final: 0.6695 (mm) REVERT: B 93 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: C 91 GLU cc_start: 0.7553 (mt-10) cc_final: 0.7258 (mt-10) REVERT: F 93 GLN cc_start: 0.7498 (OUTLIER) cc_final: 0.7239 (mt0) outliers start: 26 outliers final: 12 residues processed: 134 average time/residue: 1.7484 time to fit residues: 252.4464 Evaluate side-chains 131 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 93 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 68 ASN C 103 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16459 Z= 0.366 Angle : 0.594 7.770 23538 Z= 0.345 Chirality : 0.038 0.169 2690 Planarity : 0.004 0.038 1909 Dihedral : 28.464 78.512 4630 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.87 % Allowed : 18.10 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.31 (0.25), residues: 1141 helix: 2.14 (0.21), residues: 653 sheet: 0.02 (1.54), residues: 15 loop : -0.97 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 17 HIS 0.009 0.001 HIS L 69 PHE 0.016 0.002 PHE M 87 TYR 0.010 0.001 TYR C 49 ARG 0.006 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 116 time to evaluate : 1.291 Fit side-chains revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.6758 (mm) REVERT: N 95 VAL cc_start: 0.8606 (t) cc_final: 0.8283 (t) REVERT: B 93 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: C 91 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7208 (mt-10) REVERT: H 65 ASP cc_start: 0.8256 (t0) cc_final: 0.8044 (t0) outliers start: 29 outliers final: 15 residues processed: 135 average time/residue: 1.6791 time to fit residues: 244.3723 Evaluate side-chains 129 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 21 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 94 optimal weight: 0.5980 chunk 0 optimal weight: 50.0000 chunk 70 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 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 103 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16459 Z= 0.163 Angle : 0.513 7.314 23538 Z= 0.303 Chirality : 0.033 0.159 2690 Planarity : 0.004 0.043 1909 Dihedral : 28.096 77.041 4630 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.78 % Allowed : 19.09 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.82 (0.26), residues: 1141 helix: 2.61 (0.21), residues: 655 sheet: 0.11 (1.55), residues: 15 loop : -0.87 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP N 17 HIS 0.008 0.001 HIS L 69 PHE 0.008 0.001 PHE F 61 TYR 0.011 0.001 TYR K 24 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6674 (mm) REVERT: B 93 GLN cc_start: 0.7411 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: C 91 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7057 (mt-10) outliers start: 18 outliers final: 9 residues processed: 135 average time/residue: 1.6016 time to fit residues: 234.2582 Evaluate side-chains 128 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 137 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 11 optimal weight: 30.0000 chunk 45 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 15 HIS C 103 GLN D 81 ASN E 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16459 Z= 0.323 Angle : 0.569 9.743 23538 Z= 0.331 Chirality : 0.037 0.169 2690 Planarity : 0.004 0.037 1909 Dihedral : 28.306 77.316 4630 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.27 % Allowed : 18.89 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.25), residues: 1141 helix: 2.38 (0.21), residues: 653 sheet: -0.15 (1.48), residues: 15 loop : -0.95 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 17 HIS 0.005 0.001 HIS L 69 PHE 0.024 0.002 PHE M 38 TYR 0.010 0.001 TYR H 34 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6713 (mm) REVERT: B 93 GLN cc_start: 0.7649 (OUTLIER) cc_final: 0.7181 (mp10) REVERT: C 91 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7196 (mt-10) REVERT: E 131 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.7498 (mtp180) outliers start: 23 outliers final: 13 residues processed: 127 average time/residue: 1.6354 time to fit residues: 224.1612 Evaluate side-chains 128 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 75 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 100 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 83 optimal weight: 0.3980 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 0.7980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 15 HIS M 59 GLN C 103 GLN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16459 Z= 0.235 Angle : 0.549 9.796 23538 Z= 0.320 Chirality : 0.035 0.161 2690 Planarity : 0.004 0.035 1909 Dihedral : 28.275 77.299 4630 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.67 % Allowed : 19.29 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.25), residues: 1141 helix: 2.43 (0.21), residues: 653 sheet: -0.19 (1.46), residues: 15 loop : -0.90 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP N 17 HIS 0.004 0.001 HIS L 69 PHE 0.019 0.001 PHE M 38 TYR 0.009 0.001 TYR H 34 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 110 time to evaluate : 1.366 Fit side-chains revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6688 (mm) REVERT: B 93 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7155 (mp10) REVERT: C 91 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7131 (mt-10) REVERT: E 131 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7469 (mtp180) outliers start: 27 outliers final: 14 residues processed: 127 average time/residue: 1.6795 time to fit residues: 230.0343 Evaluate side-chains 129 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 17 MET Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 50.0000 chunk 107 optimal weight: 4.9990 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 15 HIS B 75 HIS C 103 GLN D 81 ASN E 76 GLN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 16459 Z= 0.447 Angle : 0.631 11.013 23538 Z= 0.363 Chirality : 0.040 0.176 2690 Planarity : 0.004 0.037 1909 Dihedral : 28.543 79.344 4630 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.37 % Allowed : 20.28 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.18 (0.25), residues: 1141 helix: 2.08 (0.20), residues: 653 sheet: -0.25 (1.47), residues: 15 loop : -1.09 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 17 HIS 0.004 0.001 HIS A 113 PHE 0.018 0.002 PHE M 38 TYR 0.013 0.001 TYR H 118 ARG 0.005 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 115 time to evaluate : 1.287 Fit side-chains revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6799 (mm) REVERT: B 93 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7135 (mp10) REVERT: C 91 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7261 (mt-10) REVERT: H 32 GLU cc_start: 0.7418 (pt0) cc_final: 0.7210 (pt0) outliers start: 24 outliers final: 13 residues processed: 131 average time/residue: 1.6370 time to fit residues: 231.4590 Evaluate side-chains 125 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 110 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 24 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 75 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN F 93 GLN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 16459 Z= 0.333 Angle : 0.605 10.236 23538 Z= 0.350 Chirality : 0.038 0.172 2690 Planarity : 0.004 0.038 1909 Dihedral : 28.520 79.551 4630 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.78 % Allowed : 20.97 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.25), residues: 1141 helix: 2.10 (0.20), residues: 653 sheet: -0.25 (1.46), residues: 15 loop : -1.12 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 17 HIS 0.004 0.001 HIS L 69 PHE 0.017 0.002 PHE M 38 TYR 0.011 0.001 TYR H 34 ARG 0.004 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.279 Fit side-chains revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.6782 (mm) REVERT: B 93 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.7170 (mp10) REVERT: C 91 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7233 (mt-10) REVERT: E 131 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7508 (mtp180) REVERT: H 32 GLU cc_start: 0.7399 (pt0) cc_final: 0.7191 (pt0) outliers start: 18 outliers final: 13 residues processed: 124 average time/residue: 1.6244 time to fit residues: 217.7999 Evaluate side-chains 125 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 44 VAL Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 1.9990 chunk 63 optimal weight: 0.0000 chunk 93 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS C 103 GLN D 81 ASN E 76 GLN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16459 Z= 0.170 Angle : 0.559 10.459 23538 Z= 0.327 Chirality : 0.035 0.148 2690 Planarity : 0.004 0.034 1909 Dihedral : 28.414 79.333 4630 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.19 % Allowed : 21.46 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.25), residues: 1141 helix: 2.38 (0.20), residues: 653 sheet: -0.24 (1.46), residues: 15 loop : -0.96 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP N 17 HIS 0.004 0.001 HIS L 69 PHE 0.018 0.001 PHE M 38 TYR 0.010 0.001 TYR C 49 ARG 0.004 0.000 ARG G 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: M 16 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6699 (mm) REVERT: B 93 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: C 91 GLU cc_start: 0.7361 (mt-10) cc_final: 0.7098 (mt-10) REVERT: E 131 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7450 (mtp180) outliers start: 12 outliers final: 8 residues processed: 121 average time/residue: 1.7042 time to fit residues: 222.3953 Evaluate side-chains 123 residues out of total 1011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 62 MET Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 16 optimal weight: 9.9990 chunk 31 optimal weight: 0.0040 chunk 112 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 99 optimal weight: 0.7980 chunk 6 optimal weight: 0.0050 overall best weight: 2.9610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.127611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084287 restraints weight = 28974.760| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.29 r_work: 0.3140 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16459 Z= 0.292 Angle : 0.577 10.679 23538 Z= 0.334 Chirality : 0.036 0.165 2690 Planarity : 0.004 0.036 1909 Dihedral : 28.320 79.290 4630 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.89 % Allowed : 21.96 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.49 (0.25), residues: 1141 helix: 2.35 (0.21), residues: 653 sheet: -0.17 (1.46), residues: 15 loop : -1.01 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 17 HIS 0.003 0.001 HIS L 69 PHE 0.015 0.001 PHE M 38 TYR 0.009 0.001 TYR H 34 ARG 0.004 0.000 ARG D 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4826.46 seconds wall clock time: 84 minutes 51.76 seconds (5091.76 seconds total)