Starting phenix.real_space_refine on Thu Feb 22 11:55:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/02_2024/7afl_11769_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/02_2024/7afl_11769.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/02_2024/7afl_11769_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/02_2024/7afl_11769_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/02_2024/7afl_11769_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/02_2024/7afl_11769.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/02_2024/7afl_11769.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/02_2024/7afl_11769_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afl_11769/02_2024/7afl_11769_updated.pdb" } resolution = 4.2 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= 0.005 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 P 1054 5.49 5 Mg 25 5.21 5 S 50 5.16 5 C 17386 2.51 5 N 6369 2.21 5 O 9438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34322 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 22654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1054, 22654 Classifications: {'RNA': 1054} Modifications used: {'rna2p_pur': 77, 'rna2p_pyr': 54, 'rna3p': 5, 'rna3p_pur': 530, 'rna3p_pyr': 388} Link IDs: {'rna2p': 131, 'rna3p': 922} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "R" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "V" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 783 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 3, 'TRANS': 95} Chain: "X" Number of atoms: 1174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1174 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' MG': 25} Classifications: {'undetermined': 25} Link IDs: {None: 24} Time building chain proxies: 17.80, per 1000 atoms: 0.52 Number of scatterers: 34322 At special positions: 0 Unit cell: (145.39, 211.575, 139.965, 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) S 50 16.00 P 1054 15.00 Mg 25 11.99 O 9438 8.00 N 6369 7.00 C 17386 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 25.46 Conformation dependent library (CDL) restraints added in 2.2 seconds 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2758 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 14 sheets defined 35.4% alpha, 15.3% beta 308 base pairs and 526 stacking pairs defined. Time for finding SS restraints: 20.48 Creating SS restraints... Processing helix chain 'D' and resid 8 through 15 removed outlier: 3.900A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 50 through 64 Processing helix chain 'D' and resid 69 through 81 Processing helix chain 'D' and resid 86 through 95 Processing helix chain 'D' and resid 98 through 105 Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 147 through 150 No H-bonds generated for 'chain 'D' and resid 147 through 150' Processing helix chain 'D' and resid 153 through 160 removed outlier: 4.815A pdb=" N GLU D 160 " --> pdb=" O LYS D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 109 through 118 removed outlier: 3.661A pdb=" N ALA E 118 " --> pdb=" O VAL E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 143 Processing helix chain 'E' and resid 150 through 157 Processing helix chain 'E' and resid 161 through 164 No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'F' and resid 18 through 31 removed outlier: 3.734A pdb=" N ILE F 22 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU F 23 " --> pdb=" O PRO F 19 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA F 28 " --> pdb=" O ARG F 24 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE F 29 " --> pdb=" O TYR F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 80 removed outlier: 4.046A pdb=" N ASP F 72 " --> pdb=" O GLN F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 105 removed outlier: 3.748A pdb=" N ALA F 105 " --> pdb=" O PRO F 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 101 through 105' Processing helix chain 'H' and resid 6 through 20 Processing helix chain 'H' and resid 31 through 42 Processing helix chain 'H' and resid 113 through 119 Processing helix chain 'K' and resid 48 through 50 No H-bonds generated for 'chain 'K' and resid 48 through 50' Processing helix chain 'K' and resid 55 through 58 No H-bonds generated for 'chain 'K' and resid 55 through 58' Processing helix chain 'K' and resid 60 through 77 removed outlier: 4.037A pdb=" N ALA K 67 " --> pdb=" O ALA K 63 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU K 68 " --> pdb=" O GLN K 64 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ARG K 69 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 103 Processing helix chain 'L' and resid 4 through 9 Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 114 through 117 Processing helix chain 'O' and resid 5 through 15 removed outlier: 3.543A pdb=" N GLU O 14 " --> pdb=" O LYS O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 25 through 45 removed outlier: 3.669A pdb=" N LEU O 31 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU O 45 " --> pdb=" O GLY O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 71 removed outlier: 3.872A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN O 62 " --> pdb=" O ARG O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 84 Processing helix chain 'P' and resid 54 through 63 Processing helix chain 'P' and resid 69 through 81 Processing helix chain 'Q' and resid 49 through 51 No H-bonds generated for 'chain 'Q' and resid 49 through 51' Processing helix chain 'R' and resid 13 through 16 No H-bonds generated for 'chain 'R' and resid 13 through 16' Processing helix chain 'R' and resid 26 through 31 Processing helix chain 'R' and resid 42 through 45 No H-bonds generated for 'chain 'R' and resid 42 through 45' Processing helix chain 'R' and resid 49 through 64 Processing helix chain 'T' and resid 5 through 41 removed outlier: 3.665A pdb=" N LYS T 9 " --> pdb=" O LYS T 5 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG T 10 " --> pdb=" O SER T 6 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU T 15 " --> pdb=" O ALA T 11 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG T 24 " --> pdb=" O HIS T 20 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL T 35 " --> pdb=" O PHE T 31 " (cutoff:3.500A) Processing helix chain 'T' and resid 44 through 63 Proline residue: T 56 - end of helix removed outlier: 3.513A pdb=" N ASP T 59 " --> pdb=" O GLN T 55 " (cutoff:3.500A) Processing helix chain 'T' and resid 69 through 86 Processing helix chain 'V' and resid 8 through 25 removed outlier: 4.707A pdb=" N GLN V 13 " --> pdb=" O GLN V 9 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLU V 14 " --> pdb=" O ARG V 10 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS V 17 " --> pdb=" O GLN V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 45 through 47 No H-bonds generated for 'chain 'V' and resid 45 through 47' Processing helix chain 'V' and resid 62 through 74 removed outlier: 3.654A pdb=" N ALA V 67 " --> pdb=" O ASP V 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY V 68 " --> pdb=" O ALA V 64 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 85 Processing helix chain 'X' and resid 5 through 19 removed outlier: 4.130A pdb=" N ALA X 14 " --> pdb=" O GLU X 10 " (cutoff:3.500A) Proline residue: X 15 - end of helix Processing helix chain 'X' and resid 48 through 65 removed outlier: 4.234A pdb=" N VAL X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLU X 65 " --> pdb=" O VAL X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 88 through 93 Processing sheet with id= A, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= B, first strand: chain 'E' and resid 47 through 53 removed outlier: 3.548A pdb=" N THR E 37 " --> pdb=" O GLY E 49 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL E 38 " --> pdb=" O LEU E 15 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU E 15 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY E 40 " --> pdb=" O GLU E 13 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N GLU E 13 " --> pdb=" O GLY E 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 85 through 88 Processing sheet with id= D, first strand: chain 'F' and resid 2 through 10 removed outlier: 3.643A pdb=" N VAL F 10 " --> pdb=" O HIS F 58 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 35 through 41 removed outlier: 3.545A pdb=" N LYS F 35 " --> pdb=" O GLU F 65 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASN F 63 " --> pdb=" O HIS F 37 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LEU F 39 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 61 " --> pdb=" O LEU F 39 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'H' and resid 110 through 112 removed outlier: 5.677A pdb=" N SER H 105 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ILE H 125 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 20 through 24 removed outlier: 4.348A pdb=" N VAL K 20 " --> pdb=" O THR K 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE K 31 " --> pdb=" O HIS K 24 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'K' and resid 83 through 86 removed outlier: 6.795A pdb=" N ASN K 109 " --> pdb=" O VAL K 84 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N VAL K 86 " --> pdb=" O ASN K 109 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N THR K 111 " --> pdb=" O VAL K 86 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'L' and resid 95 through 98 removed outlier: 4.874A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE L 82 " --> pdb=" O LYS L 30 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS L 30 " --> pdb=" O ILE L 82 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ARG L 54 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL L 37 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N VAL L 52 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR L 39 " --> pdb=" O ARG L 50 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ARG L 50 " --> pdb=" O THR L 39 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'P' and resid 3 through 5 removed outlier: 6.730A pdb=" N VAL P 21 " --> pdb=" O ARG P 35 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ARG P 35 " --> pdb=" O VAL P 21 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Q' and resid 58 through 62 removed outlier: 16.048A pdb=" N THR Q 7 " --> pdb=" O PHE Q 28 " (cutoff:3.500A) removed outlier: 12.585A pdb=" N PHE Q 28 " --> pdb=" O THR Q 7 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLN Q 9 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLU Q 26 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL Q 22 " --> pdb=" O VAL Q 13 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'V' and resid 94 through 98 removed outlier: 6.181A pdb=" N THR V 55 " --> pdb=" O VAL V 38 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N VAL V 38 " --> pdb=" O THR V 55 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'X' and resid 75 through 77 removed outlier: 6.135A pdb=" N ASP X 41 " --> pdb=" O LEU X 23 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LEU X 23 " --> pdb=" O ASP X 41 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'X' and resid 143 through 146 removed outlier: 6.894A pdb=" N THR X 126 " --> pdb=" O LYS X 118 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 695 hydrogen bonds 826 hydrogen bond angles 0 basepair planarities 308 basepair parallelities 526 stacking parallelities Total time for adding SS restraints: 24.03 Time building geometry restraints manager: 25.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5139 1.33 - 1.45: 15363 1.45 - 1.57: 14482 1.57 - 1.70: 2103 1.70 - 1.82: 88 Bond restraints: 37175 Sorted by residual: bond pdb=" O3' U A 571 " pdb=" P A A 572 " ideal model delta sigma weight residual 1.607 1.469 0.138 1.50e-02 4.44e+03 8.44e+01 bond pdb=" C2 G7M A 527 " pdb=" N3 G7M A 527 " ideal model delta sigma weight residual 1.462 1.313 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" N3 2MG A1516 " pdb=" C4 2MG A1516 " ideal model delta sigma weight residual 1.496 1.347 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C2 2MG A1516 " pdb=" N2 2MG A1516 " ideal model delta sigma weight residual 1.475 1.340 0.135 2.00e-02 2.50e+03 4.58e+01 bond pdb=" N3 G7M A 527 " pdb=" C4 G7M A 527 " ideal model delta sigma weight residual 1.492 1.358 0.134 2.00e-02 2.50e+03 4.52e+01 ... (remaining 37170 not shown) Histogram of bond angle deviations from ideal: 97.95 - 105.95: 5784 105.95 - 113.96: 23806 113.96 - 121.96: 17744 121.96 - 129.97: 7441 129.97 - 137.97: 668 Bond angle restraints: 55443 Sorted by residual: angle pdb=" C1' G7M A 527 " pdb=" N9 G7M A 527 " pdb=" C8 G7M A 527 " ideal model delta sigma weight residual 94.96 129.36 -34.40 3.00e+00 1.11e-01 1.31e+02 angle pdb=" C ILE V 91 " pdb=" N VAL V 92 " pdb=" CA VAL V 92 " ideal model delta sigma weight residual 122.60 117.89 4.71 6.80e-01 2.16e+00 4.80e+01 angle pdb=" C LYS H 56 " pdb=" CA LYS H 56 " pdb=" CB LYS H 56 " ideal model delta sigma weight residual 111.00 116.99 -5.99 8.70e-01 1.32e+00 4.74e+01 angle pdb=" CA PRO V 30 " pdb=" N PRO V 30 " pdb=" CD PRO V 30 " ideal model delta sigma weight residual 112.00 103.40 8.60 1.40e+00 5.10e-01 3.77e+01 angle pdb=" N PRO H 28 " pdb=" CA PRO H 28 " pdb=" C PRO H 28 " ideal model delta sigma weight residual 111.03 102.01 9.02 1.54e+00 4.22e-01 3.43e+01 ... (remaining 55438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 20551 35.61 - 71.23: 2890 71.23 - 106.84: 325 106.84 - 142.45: 11 142.45 - 178.07: 6 Dihedral angle restraints: 23783 sinusoidal: 19513 harmonic: 4270 Sorted by residual: dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 46.47 153.53 1 1.50e+01 4.44e-03 8.09e+01 dihedral pdb=" O4' C A 754 " pdb=" C1' C A 754 " pdb=" N1 C A 754 " pdb=" C2 C A 754 " ideal model delta sinusoidal sigma weight residual 200.00 51.18 148.82 1 1.50e+01 4.44e-03 7.92e+01 dihedral pdb=" O4' C A 183 " pdb=" C1' C A 183 " pdb=" N1 C A 183 " pdb=" C2 C A 183 " ideal model delta sinusoidal sigma weight residual -128.00 50.07 -178.07 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 23780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 5946 0.082 - 0.164: 861 0.164 - 0.246: 214 0.246 - 0.327: 27 0.327 - 0.409: 6 Chirality restraints: 7054 Sorted by residual: chirality pdb=" CA ASN D 89 " pdb=" N ASN D 89 " pdb=" C ASN D 89 " pdb=" CB ASN D 89 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ASN T 52 " pdb=" N ASN T 52 " pdb=" C ASN T 52 " pdb=" CB ASN T 52 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" CA VAL K 32 " pdb=" N VAL K 32 " pdb=" C VAL K 32 " pdb=" CB VAL K 32 " both_signs ideal model delta sigma weight residual False 2.44 2.81 -0.37 2.00e-01 2.50e+01 3.35e+00 ... (remaining 7051 not shown) Planarity restraints: 3113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " 0.060 2.00e-02 2.50e+03 5.84e-01 7.69e+03 pdb=" C4' 2MG A1516 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " 0.571 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " -0.632 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " -0.170 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " 0.978 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " 0.230 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " -0.877 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG A1516 " 0.096 2.00e-02 2.50e+03 1.84e-01 1.10e+03 pdb=" N9 2MG A1516 " 0.009 2.00e-02 2.50e+03 pdb=" C8 2MG A1516 " -0.089 2.00e-02 2.50e+03 pdb=" N7 2MG A1516 " -0.121 2.00e-02 2.50e+03 pdb=" C5 2MG A1516 " -0.035 2.00e-02 2.50e+03 pdb=" C6 2MG A1516 " -0.011 2.00e-02 2.50e+03 pdb=" O6 2MG A1516 " -0.086 2.00e-02 2.50e+03 pdb=" N1 2MG A1516 " 0.093 2.00e-02 2.50e+03 pdb=" C2 2MG A1516 " 0.182 2.00e-02 2.50e+03 pdb=" N2 2MG A1516 " 0.265 2.00e-02 2.50e+03 pdb=" N3 2MG A1516 " 0.157 2.00e-02 2.50e+03 pdb=" C4 2MG A1516 " 0.053 2.00e-02 2.50e+03 pdb=" CM2 2MG A1516 " -0.512 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 MA6 A1519 " 0.134 2.00e-02 2.50e+03 2.18e-01 4.76e+02 pdb=" N6 MA6 A1519 " -0.378 2.00e-02 2.50e+03 pdb=" C10 MA6 A1519 " 0.122 2.00e-02 2.50e+03 pdb=" C9 MA6 A1519 " 0.122 2.00e-02 2.50e+03 ... (remaining 3110 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 648 2.46 - 3.07: 26349 3.07 - 3.68: 78460 3.68 - 4.29: 102394 4.29 - 4.90: 134557 Nonbonded interactions: 342408 Sorted by model distance: nonbonded pdb=" OP2 A A 116 " pdb="MG MG A1625 " model vdw 1.852 2.170 nonbonded pdb=" OP2 A A 53 " pdb="MG MG A1613 " model vdw 1.883 2.170 nonbonded pdb=" OP2 G A 289 " pdb="MG MG A1625 " model vdw 1.890 2.170 nonbonded pdb=" O3' C A1521 " pdb="MG MG A1622 " model vdw 1.899 2.170 nonbonded pdb=" OP1 A A 547 " pdb="MG MG A1614 " model vdw 1.909 2.170 ... (remaining 342403 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 14.140 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 119.830 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.149 37175 Z= 0.617 Angle : 1.088 34.397 55443 Z= 0.678 Chirality : 0.065 0.409 7054 Planarity : 0.013 0.584 3113 Dihedral : 24.589 178.066 21025 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 43.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Cbeta Deviations : 0.44 % 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: -1.84 (0.20), residues: 1458 helix: -0.77 (0.23), residues: 495 sheet: -1.05 (0.32), residues: 250 loop : -1.55 (0.21), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.004 TRP F 42 HIS 0.011 0.002 HIS Q 47 PHE 0.023 0.002 PHE X 94 TYR 0.016 0.002 TYR L 95 ARG 0.035 0.001 ARG V 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 422 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 22 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7819 (mmmt) REVERT: D 51 TYR cc_start: 0.9026 (t80) cc_final: 0.8715 (t80) REVERT: D 71 GLN cc_start: 0.9255 (tt0) cc_final: 0.8881 (tp40) REVERT: D 72 PHE cc_start: 0.9611 (t80) cc_final: 0.9052 (t80) REVERT: D 74 ASN cc_start: 0.9073 (m-40) cc_final: 0.8821 (m110) REVERT: D 103 TYR cc_start: 0.8538 (t80) cc_final: 0.8125 (t80) REVERT: D 204 TYR cc_start: 0.8560 (m-80) cc_final: 0.7993 (m-80) REVERT: E 13 GLU cc_start: 0.9353 (pm20) cc_final: 0.9137 (pm20) REVERT: E 14 LYS cc_start: 0.8985 (tttm) cc_final: 0.8593 (mtmm) REVERT: E 30 ILE cc_start: 0.9048 (mm) cc_final: 0.8667 (mm) REVERT: E 31 PHE cc_start: 0.9383 (m-80) cc_final: 0.8994 (m-10) REVERT: E 62 LYS cc_start: 0.9426 (mtmt) cc_final: 0.9181 (mmtt) REVERT: E 68 ARG cc_start: 0.9299 (mmt-90) cc_final: 0.8674 (mmm160) REVERT: E 71 MET cc_start: 0.7894 (mtp) cc_final: 0.7054 (mtp) REVERT: F 13 ASP cc_start: 0.9397 (p0) cc_final: 0.9052 (p0) REVERT: F 14 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8411 (tm-30) REVERT: F 54 LEU cc_start: 0.9066 (mt) cc_final: 0.8776 (mt) REVERT: F 88 MET cc_start: 0.8628 (tmm) cc_final: 0.7361 (tmm) REVERT: F 89 VAL cc_start: 0.9233 (t) cc_final: 0.8992 (t) REVERT: F 90 MET cc_start: 0.8825 (mtm) cc_final: 0.8569 (tpp) REVERT: F 102 MET cc_start: 0.9000 (mmp) cc_final: 0.8768 (mmp) REVERT: H 39 VAL cc_start: 0.9608 (t) cc_final: 0.9173 (t) REVERT: H 45 PHE cc_start: 0.8580 (m-80) cc_final: 0.6931 (m-80) REVERT: H 59 LEU cc_start: 0.9302 (tp) cc_final: 0.9047 (tp) REVERT: H 89 LYS cc_start: 0.8915 (ptmm) cc_final: 0.8668 (ptpp) REVERT: H 113 ASP cc_start: 0.9307 (p0) cc_final: 0.8995 (p0) REVERT: H 121 LEU cc_start: 0.8960 (mt) cc_final: 0.8684 (tt) REVERT: H 125 ILE cc_start: 0.9417 (mt) cc_final: 0.9144 (mp) REVERT: H 126 ILE cc_start: 0.9629 (mm) cc_final: 0.9139 (mt) REVERT: K 38 GLN cc_start: 0.9147 (mt0) cc_final: 0.8936 (pp30) REVERT: K 79 ILE cc_start: 0.8899 (mt) cc_final: 0.8274 (mp) REVERT: K 85 MET cc_start: 0.8783 (mtp) cc_final: 0.8440 (mpp) REVERT: L 112 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8677 (mp10) REVERT: O 65 LYS cc_start: 0.9651 (mttt) cc_final: 0.9357 (mmtt) REVERT: O 87 LEU cc_start: 0.9079 (mt) cc_final: 0.8784 (mt) REVERT: P 3 THR cc_start: 0.8225 (t) cc_final: 0.7973 (p) REVERT: P 12 LYS cc_start: 0.8786 (ttmt) cc_final: 0.8368 (ttpp) REVERT: P 75 ILE cc_start: 0.9680 (mp) cc_final: 0.9256 (tp) REVERT: Q 15 ASP cc_start: 0.9008 (p0) cc_final: 0.8679 (p0) REVERT: Q 55 ILE cc_start: 0.8609 (pt) cc_final: 0.8038 (mp) REVERT: Q 57 ASP cc_start: 0.8769 (m-30) cc_final: 0.8527 (m-30) REVERT: Q 69 LYS cc_start: 0.9070 (mmmt) cc_final: 0.8719 (ttpt) REVERT: R 22 ASP cc_start: 0.7839 (t0) cc_final: 0.7586 (t0) REVERT: R 23 TYR cc_start: 0.9260 (p90) cc_final: 0.8921 (p90) REVERT: R 60 LYS cc_start: 0.9435 (mttt) cc_final: 0.9163 (mtpp) REVERT: R 61 ARG cc_start: 0.8877 (mtt180) cc_final: 0.8373 (mmt90) REVERT: T 27 MET cc_start: 0.9523 (tmm) cc_final: 0.9013 (tmm) REVERT: T 86 LEU cc_start: 0.8433 (mm) cc_final: 0.8232 (mm) REVERT: V 16 GLN cc_start: 0.9249 (mt0) cc_final: 0.8645 (mp10) REVERT: V 42 GLU cc_start: 0.8711 (tp30) cc_final: 0.8392 (mm-30) REVERT: X 30 ARG cc_start: 0.7333 (ttm110) cc_final: 0.6971 (tpt90) REVERT: X 62 LEU cc_start: 0.9180 (tp) cc_final: 0.8548 (pp) REVERT: X 66 ASP cc_start: 0.8691 (t0) cc_final: 0.8216 (t0) REVERT: X 73 ASN cc_start: 0.9191 (t0) cc_final: 0.8547 (m-40) REVERT: X 145 ASN cc_start: 0.9039 (t0) cc_final: 0.8648 (t0) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.5763 time to fit residues: 362.3477 Evaluate side-chains 265 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 208 optimal weight: 10.0000 chunk 187 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 36 GLN D 126 ASN E 70 ASN E 73 ASN E 83 HIS ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN L 5 ASN L 72 HIS O 37 ASN ** P 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN R 52 GLN V 16 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37175 Z= 0.249 Angle : 0.689 13.399 55443 Z= 0.356 Chirality : 0.037 0.274 7054 Planarity : 0.006 0.114 3113 Dihedral : 25.116 179.679 18122 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 32.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.08 % Allowed : 4.80 % Favored : 95.12 % 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: -1.43 (0.21), residues: 1458 helix: -0.70 (0.21), residues: 521 sheet: -0.86 (0.30), residues: 280 loop : -1.04 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P 60 HIS 0.006 0.001 HIS X 56 PHE 0.022 0.002 PHE H 45 TYR 0.020 0.002 TYR D 76 ARG 0.016 0.001 ARG V 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 326 time to evaluate : 2.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 PHE cc_start: 0.9100 (m-80) cc_final: 0.8872 (m-80) REVERT: D 51 TYR cc_start: 0.9069 (t80) cc_final: 0.8773 (t80) REVERT: D 71 GLN cc_start: 0.9070 (tt0) cc_final: 0.8707 (tp-100) REVERT: D 72 PHE cc_start: 0.9585 (t80) cc_final: 0.9183 (t80) REVERT: D 103 TYR cc_start: 0.8771 (t80) cc_final: 0.8343 (t80) REVERT: E 41 ASP cc_start: 0.7460 (m-30) cc_final: 0.6618 (m-30) REVERT: E 62 LYS cc_start: 0.9385 (mtmt) cc_final: 0.9135 (mmtt) REVERT: E 71 MET cc_start: 0.7708 (mtp) cc_final: 0.6164 (mtp) REVERT: E 96 MET cc_start: 0.9080 (mmp) cc_final: 0.8864 (mmp) REVERT: F 16 GLU cc_start: 0.8860 (pm20) cc_final: 0.8258 (pm20) REVERT: F 62 MET cc_start: 0.8555 (mpp) cc_final: 0.8317 (mpp) REVERT: F 88 MET cc_start: 0.8531 (tmm) cc_final: 0.7397 (tmm) REVERT: F 90 MET cc_start: 0.8725 (mtm) cc_final: 0.8509 (tpt) REVERT: H 7 ILE cc_start: 0.9664 (mm) cc_final: 0.9393 (mp) REVERT: H 27 MET cc_start: 0.8512 (pmm) cc_final: 0.8227 (pmm) REVERT: H 99 LEU cc_start: 0.9358 (mp) cc_final: 0.9025 (mt) REVERT: H 113 ASP cc_start: 0.9160 (p0) cc_final: 0.8946 (p0) REVERT: H 121 LEU cc_start: 0.8988 (mt) cc_final: 0.8460 (tt) REVERT: L 81 LEU cc_start: 0.8556 (mm) cc_final: 0.8328 (mm) REVERT: L 112 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8724 (mp10) REVERT: O 65 LYS cc_start: 0.9574 (mttt) cc_final: 0.9334 (tmmt) REVERT: O 68 ASP cc_start: 0.9590 (m-30) cc_final: 0.9373 (m-30) REVERT: P 3 THR cc_start: 0.8309 (t) cc_final: 0.8044 (p) REVERT: P 12 LYS cc_start: 0.8803 (ttmt) cc_final: 0.8499 (ttpp) REVERT: P 18 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8406 (mp10) REVERT: P 23 ASP cc_start: 0.7863 (t70) cc_final: 0.7637 (t70) REVERT: Q 15 ASP cc_start: 0.8851 (p0) cc_final: 0.8486 (p0) REVERT: Q 17 MET cc_start: 0.8501 (mpp) cc_final: 0.8066 (mpp) REVERT: Q 55 ILE cc_start: 0.8344 (pt) cc_final: 0.7819 (mp) REVERT: R 61 ARG cc_start: 0.8820 (mtt180) cc_final: 0.8561 (mtt180) REVERT: T 27 MET cc_start: 0.9473 (tmm) cc_final: 0.9263 (tmm) REVERT: T 54 MET cc_start: 0.8914 (tmm) cc_final: 0.8688 (tmm) REVERT: V 16 GLN cc_start: 0.9115 (mt0) cc_final: 0.8655 (mp10) REVERT: V 43 MET cc_start: 0.8718 (mmt) cc_final: 0.8345 (mmm) REVERT: V 51 LYS cc_start: 0.8646 (mmpt) cc_final: 0.8291 (mmtm) REVERT: V 62 GLU cc_start: 0.8870 (tp30) cc_final: 0.8332 (tp30) REVERT: X 62 LEU cc_start: 0.9330 (tp) cc_final: 0.8642 (pp) REVERT: X 109 ASN cc_start: 0.8680 (p0) cc_final: 0.8319 (p0) REVERT: X 117 ILE cc_start: 0.9375 (mt) cc_final: 0.9063 (tp) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.5504 time to fit residues: 274.8107 Evaluate side-chains 237 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 124 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 224 optimal weight: 0.9980 chunk 242 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 180 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 ASN ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 47 ASN ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 37175 Z= 0.318 Angle : 0.678 11.737 55443 Z= 0.351 Chirality : 0.037 0.240 7054 Planarity : 0.006 0.120 3113 Dihedral : 24.933 179.974 18122 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 36.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.08 % Allowed : 7.08 % Favored : 92.84 % 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: -1.33 (0.21), residues: 1458 helix: -0.48 (0.21), residues: 522 sheet: -1.15 (0.28), residues: 311 loop : -0.90 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 60 HIS 0.009 0.002 HIS L 77 PHE 0.021 0.003 PHE H 45 TYR 0.025 0.002 TYR L 95 ARG 0.012 0.001 ARG V 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 2.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 PHE cc_start: 0.9079 (m-80) cc_final: 0.8862 (m-80) REVERT: D 51 TYR cc_start: 0.8965 (t80) cc_final: 0.8705 (t80) REVERT: D 71 GLN cc_start: 0.9075 (tt0) cc_final: 0.8241 (tp-100) REVERT: D 72 PHE cc_start: 0.9611 (t80) cc_final: 0.9015 (t80) REVERT: D 75 TYR cc_start: 0.8825 (m-80) cc_final: 0.7812 (m-80) REVERT: D 103 TYR cc_start: 0.8745 (t80) cc_final: 0.8405 (t80) REVERT: E 20 ARG cc_start: 0.9388 (ttt-90) cc_final: 0.9023 (ttt-90) REVERT: E 41 ASP cc_start: 0.7092 (m-30) cc_final: 0.6312 (m-30) REVERT: E 64 MET cc_start: 0.9574 (ptt) cc_final: 0.9321 (ptp) REVERT: E 65 GLU cc_start: 0.8357 (pt0) cc_final: 0.8037 (pt0) REVERT: E 71 MET cc_start: 0.7758 (mtp) cc_final: 0.6088 (mtp) REVERT: F 1 MET cc_start: 0.7440 (ptm) cc_final: 0.7063 (ptm) REVERT: F 73 GLU cc_start: 0.9121 (mp0) cc_final: 0.8888 (mp0) REVERT: F 75 GLU cc_start: 0.9165 (pp20) cc_final: 0.8887 (pp20) REVERT: F 88 MET cc_start: 0.8672 (tmm) cc_final: 0.7783 (tmm) REVERT: F 102 MET cc_start: 0.9323 (mpp) cc_final: 0.8743 (mpp) REVERT: H 10 MET cc_start: 0.9595 (tmm) cc_final: 0.9189 (tmm) REVERT: H 11 LEU cc_start: 0.9637 (mt) cc_final: 0.9283 (mt) REVERT: H 27 MET cc_start: 0.8538 (pmm) cc_final: 0.8236 (pmm) REVERT: H 91 GLU cc_start: 0.9249 (pt0) cc_final: 0.9038 (pt0) REVERT: H 99 LEU cc_start: 0.9285 (mp) cc_final: 0.9084 (mt) REVERT: H 113 ASP cc_start: 0.9153 (p0) cc_final: 0.8902 (p0) REVERT: H 121 LEU cc_start: 0.9077 (mt) cc_final: 0.8621 (tt) REVERT: K 38 GLN cc_start: 0.7955 (pp30) cc_final: 0.7705 (pp30) REVERT: K 75 LYS cc_start: 0.8638 (mtmm) cc_final: 0.8419 (mmmt) REVERT: K 85 MET cc_start: 0.8232 (mpp) cc_final: 0.7843 (mpp) REVERT: L 38 TYR cc_start: 0.9249 (p90) cc_final: 0.8831 (p90) REVERT: L 73 ASN cc_start: 0.9273 (m-40) cc_final: 0.8855 (p0) REVERT: L 112 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8694 (mp10) REVERT: O 65 LYS cc_start: 0.9621 (mttt) cc_final: 0.9330 (tmmt) REVERT: O 68 ASP cc_start: 0.9641 (m-30) cc_final: 0.9401 (m-30) REVERT: O 87 LEU cc_start: 0.9132 (mt) cc_final: 0.8882 (mt) REVERT: P 12 LYS cc_start: 0.8936 (ttmt) cc_final: 0.8524 (ttpp) REVERT: P 26 ASN cc_start: 0.9020 (m110) cc_final: 0.8768 (m110) REVERT: Q 11 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8343 (ttp80) REVERT: Q 15 ASP cc_start: 0.8849 (p0) cc_final: 0.8489 (p0) REVERT: Q 27 ARG cc_start: 0.8942 (ptt-90) cc_final: 0.8503 (ptt-90) REVERT: Q 42 THR cc_start: 0.8298 (p) cc_final: 0.7074 (p) REVERT: Q 43 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8150 (mtpt) REVERT: Q 55 ILE cc_start: 0.8475 (pt) cc_final: 0.7949 (mp) REVERT: T 51 PHE cc_start: 0.9275 (t80) cc_final: 0.8964 (t80) REVERT: T 54 MET cc_start: 0.8949 (tmm) cc_final: 0.8743 (tmm) REVERT: V 16 GLN cc_start: 0.8953 (mt0) cc_final: 0.8440 (pt0) REVERT: V 35 MET cc_start: 0.8521 (ppp) cc_final: 0.8317 (ppp) REVERT: V 51 LYS cc_start: 0.8534 (mmpt) cc_final: 0.8174 (mtpp) REVERT: X 37 ARG cc_start: 0.8769 (mtm180) cc_final: 0.8389 (mtm-85) REVERT: X 109 ASN cc_start: 0.8698 (p0) cc_final: 0.8290 (p0) outliers start: 1 outliers final: 1 residues processed: 291 average time/residue: 0.5465 time to fit residues: 245.4261 Evaluate side-chains 230 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 222 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 107 optimal weight: 0.0270 chunk 150 optimal weight: 10.0000 chunk 225 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 chunk 213 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 overall best weight: 5.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 37175 Z= 0.257 Angle : 0.616 11.702 55443 Z= 0.322 Chirality : 0.035 0.242 7054 Planarity : 0.005 0.118 3113 Dihedral : 24.812 178.888 18122 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 32.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.16 (0.21), residues: 1458 helix: -0.31 (0.21), residues: 518 sheet: -1.13 (0.28), residues: 305 loop : -0.79 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P 60 HIS 0.006 0.002 HIS X 56 PHE 0.024 0.002 PHE F 8 TYR 0.021 0.002 TYR L 95 ARG 0.006 0.001 ARG V 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 20 PHE cc_start: 0.9092 (m-80) cc_final: 0.8804 (m-80) REVERT: D 51 TYR cc_start: 0.8957 (t80) cc_final: 0.8671 (t80) REVERT: D 71 GLN cc_start: 0.9029 (tt0) cc_final: 0.8286 (tp-100) REVERT: D 72 PHE cc_start: 0.9625 (t80) cc_final: 0.9027 (t80) REVERT: D 75 TYR cc_start: 0.8771 (m-80) cc_final: 0.7865 (m-80) REVERT: D 103 TYR cc_start: 0.8753 (t80) cc_final: 0.8402 (t80) REVERT: D 124 MET cc_start: 0.8237 (mmp) cc_final: 0.7677 (mmp) REVERT: E 16 ILE cc_start: 0.9507 (mp) cc_final: 0.9221 (mp) REVERT: E 24 THR cc_start: 0.7871 (m) cc_final: 0.7597 (p) REVERT: E 31 PHE cc_start: 0.9297 (m-80) cc_final: 0.8871 (m-80) REVERT: E 41 ASP cc_start: 0.7255 (m-30) cc_final: 0.6375 (m-30) REVERT: E 65 GLU cc_start: 0.8378 (pt0) cc_final: 0.8024 (pt0) REVERT: E 71 MET cc_start: 0.8022 (mtp) cc_final: 0.6655 (mtp) REVERT: F 44 ARG cc_start: 0.8705 (mpp-170) cc_final: 0.8450 (mpp80) REVERT: F 72 ASP cc_start: 0.9193 (m-30) cc_final: 0.8899 (m-30) REVERT: F 75 GLU cc_start: 0.9142 (pp20) cc_final: 0.8898 (pp20) REVERT: F 88 MET cc_start: 0.8507 (tmm) cc_final: 0.7700 (tmm) REVERT: F 90 MET cc_start: 0.8359 (mtm) cc_final: 0.8143 (mtp) REVERT: F 102 MET cc_start: 0.9352 (mpp) cc_final: 0.8825 (mpp) REVERT: H 10 MET cc_start: 0.9564 (tmm) cc_final: 0.9143 (ppp) REVERT: H 11 LEU cc_start: 0.9661 (mt) cc_final: 0.9362 (mt) REVERT: H 27 MET cc_start: 0.8573 (pmm) cc_final: 0.8221 (pmm) REVERT: H 86 TYR cc_start: 0.8614 (m-80) cc_final: 0.8158 (m-80) REVERT: H 113 ASP cc_start: 0.9149 (p0) cc_final: 0.8849 (p0) REVERT: H 121 LEU cc_start: 0.9233 (mt) cc_final: 0.8844 (tt) REVERT: L 38 TYR cc_start: 0.9197 (p90) cc_final: 0.8559 (p90) REVERT: L 73 ASN cc_start: 0.9277 (m-40) cc_final: 0.8844 (p0) REVERT: L 103 ASP cc_start: 0.8854 (t0) cc_final: 0.8139 (t0) REVERT: L 112 GLN cc_start: 0.9085 (mm-40) cc_final: 0.8666 (mp10) REVERT: O 87 LEU cc_start: 0.9188 (mt) cc_final: 0.8966 (mt) REVERT: P 26 ASN cc_start: 0.8977 (m110) cc_final: 0.8751 (m110) REVERT: P 56 ARG cc_start: 0.9514 (tpm170) cc_final: 0.9212 (mmm160) REVERT: P 76 LYS cc_start: 0.9526 (tmtt) cc_final: 0.9010 (tptm) REVERT: Q 15 ASP cc_start: 0.8842 (p0) cc_final: 0.8534 (p0) REVERT: Q 17 MET cc_start: 0.8514 (mpp) cc_final: 0.8098 (mpp) REVERT: Q 27 ARG cc_start: 0.8998 (ptt-90) cc_final: 0.8550 (ptt-90) REVERT: Q 55 ILE cc_start: 0.8390 (pt) cc_final: 0.7922 (mp) REVERT: T 51 PHE cc_start: 0.9232 (t80) cc_final: 0.8969 (t80) REVERT: V 16 GLN cc_start: 0.8942 (mt0) cc_final: 0.8460 (pt0) REVERT: V 35 MET cc_start: 0.8669 (ppp) cc_final: 0.8453 (ppp) REVERT: X 37 ARG cc_start: 0.9285 (mpp80) cc_final: 0.8901 (mtm-85) REVERT: X 109 ASN cc_start: 0.8536 (p0) cc_final: 0.7989 (p0) REVERT: X 117 ILE cc_start: 0.9371 (mt) cc_final: 0.9087 (tp) outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.5277 time to fit residues: 239.4967 Evaluate side-chains 224 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 198 optimal weight: 0.6980 chunk 135 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 177 optimal weight: 0.2980 chunk 98 optimal weight: 20.0000 chunk 203 optimal weight: 9.9990 chunk 165 optimal weight: 0.0670 chunk 0 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 214 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 overall best weight: 1.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 37 HIS F 46 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN T 61 GLN V 73 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 37175 Z= 0.142 Angle : 0.550 11.806 55443 Z= 0.288 Chirality : 0.032 0.239 7054 Planarity : 0.004 0.115 3113 Dihedral : 24.521 179.388 18122 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.08 % Allowed : 3.58 % Favored : 96.34 % 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: -0.97 (0.21), residues: 1458 helix: -0.07 (0.21), residues: 537 sheet: -1.01 (0.30), residues: 279 loop : -0.83 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X 113 HIS 0.008 0.001 HIS F 58 PHE 0.024 0.002 PHE F 78 TYR 0.019 0.001 TYR L 95 ARG 0.006 0.000 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 2.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLN cc_start: 0.8933 (tt0) cc_final: 0.8218 (tp-100) REVERT: D 72 PHE cc_start: 0.9582 (t80) cc_final: 0.8728 (t80) REVERT: D 75 TYR cc_start: 0.8752 (m-80) cc_final: 0.7842 (m-80) REVERT: D 124 MET cc_start: 0.8175 (mmp) cc_final: 0.7696 (mmp) REVERT: E 24 THR cc_start: 0.7850 (m) cc_final: 0.7573 (p) REVERT: E 31 PHE cc_start: 0.9312 (m-80) cc_final: 0.9010 (m-80) REVERT: E 41 ASP cc_start: 0.7173 (m-30) cc_final: 0.6291 (m-30) REVERT: E 65 GLU cc_start: 0.8535 (pt0) cc_final: 0.8100 (pt0) REVERT: E 71 MET cc_start: 0.7986 (mtp) cc_final: 0.6692 (mtp) REVERT: E 112 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8407 (tpp80) REVERT: E 163 GLU cc_start: 0.9283 (tt0) cc_final: 0.8975 (mt-10) REVERT: F 69 GLU cc_start: 0.9086 (pm20) cc_final: 0.8833 (pm20) REVERT: F 72 ASP cc_start: 0.9134 (m-30) cc_final: 0.8863 (m-30) REVERT: F 73 GLU cc_start: 0.8997 (mp0) cc_final: 0.8774 (mp0) REVERT: F 75 GLU cc_start: 0.9086 (pp20) cc_final: 0.8811 (pp20) REVERT: F 88 MET cc_start: 0.8463 (tmm) cc_final: 0.7923 (tmm) REVERT: F 102 MET cc_start: 0.9300 (mpp) cc_final: 0.8957 (mpp) REVERT: H 10 MET cc_start: 0.9563 (tmm) cc_final: 0.9159 (ppp) REVERT: H 11 LEU cc_start: 0.9621 (mt) cc_final: 0.9339 (mt) REVERT: H 27 MET cc_start: 0.8730 (pmm) cc_final: 0.8499 (pmm) REVERT: H 75 ILE cc_start: 0.9457 (pt) cc_final: 0.9229 (pt) REVERT: H 80 ARG cc_start: 0.8705 (mtp-110) cc_final: 0.8417 (mtp-110) REVERT: H 107 SER cc_start: 0.9488 (m) cc_final: 0.8881 (t) REVERT: H 113 ASP cc_start: 0.9088 (p0) cc_final: 0.8794 (p0) REVERT: H 121 LEU cc_start: 0.9278 (mt) cc_final: 0.8963 (tp) REVERT: H 125 ILE cc_start: 0.9438 (tt) cc_final: 0.9232 (tt) REVERT: K 85 MET cc_start: 0.8741 (mmp) cc_final: 0.8528 (mmp) REVERT: L 38 TYR cc_start: 0.9215 (p90) cc_final: 0.8780 (p90) REVERT: L 73 ASN cc_start: 0.9275 (m-40) cc_final: 0.8959 (p0) REVERT: L 112 GLN cc_start: 0.9037 (mm-40) cc_final: 0.8637 (mp10) REVERT: O 68 ASP cc_start: 0.9508 (m-30) cc_final: 0.9250 (m-30) REVERT: P 17 TYR cc_start: 0.8256 (m-80) cc_final: 0.7477 (m-80) REVERT: P 18 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8489 (mp10) REVERT: P 56 ARG cc_start: 0.9388 (tpm170) cc_final: 0.9133 (mmm160) REVERT: P 76 LYS cc_start: 0.9564 (tmtt) cc_final: 0.9258 (tmtt) REVERT: Q 8 LEU cc_start: 0.9516 (tp) cc_final: 0.9038 (tp) REVERT: Q 11 ARG cc_start: 0.8638 (ttp80) cc_final: 0.8335 (ttp80) REVERT: Q 15 ASP cc_start: 0.8825 (p0) cc_final: 0.8511 (p0) REVERT: Q 25 ILE cc_start: 0.9147 (mp) cc_final: 0.8862 (mp) REVERT: Q 27 ARG cc_start: 0.8952 (ptt-90) cc_final: 0.8553 (ptt-90) REVERT: Q 42 THR cc_start: 0.8545 (p) cc_final: 0.7664 (p) REVERT: Q 55 ILE cc_start: 0.8655 (pt) cc_final: 0.8138 (mp) REVERT: T 28 MET cc_start: 0.9082 (tpp) cc_final: 0.8782 (mmt) REVERT: T 51 PHE cc_start: 0.9264 (t80) cc_final: 0.9019 (t80) REVERT: V 16 GLN cc_start: 0.8975 (mt0) cc_final: 0.8476 (pt0) REVERT: X 1 MET cc_start: 0.0613 (mtt) cc_final: -0.0066 (mtt) REVERT: X 37 ARG cc_start: 0.9256 (mpp80) cc_final: 0.8840 (mtm-85) REVERT: X 66 ASP cc_start: 0.8766 (t0) cc_final: 0.8437 (t0) REVERT: X 109 ASN cc_start: 0.8442 (p0) cc_final: 0.7784 (p0) outliers start: 1 outliers final: 0 residues processed: 307 average time/residue: 0.5223 time to fit residues: 248.3521 Evaluate side-chains 228 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 80 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 58 optimal weight: 10.0000 chunk 238 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 79 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 37175 Z= 0.252 Angle : 0.598 11.683 55443 Z= 0.312 Chirality : 0.034 0.244 7054 Planarity : 0.005 0.117 3113 Dihedral : 24.500 179.922 18122 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 31.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: -0.94 (0.22), residues: 1458 helix: -0.15 (0.21), residues: 537 sheet: -1.01 (0.29), residues: 290 loop : -0.67 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP X 113 HIS 0.007 0.002 HIS X 56 PHE 0.017 0.002 PHE F 78 TYR 0.019 0.002 TYR L 95 ARG 0.008 0.001 ARG R 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 276 time to evaluate : 2.062 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: D 71 GLN cc_start: 0.8941 (tt0) cc_final: 0.8170 (tp-100) REVERT: D 72 PHE cc_start: 0.9628 (t80) cc_final: 0.8776 (t80) REVERT: D 75 TYR cc_start: 0.8783 (m-80) cc_final: 0.7749 (m-80) REVERT: D 124 MET cc_start: 0.8212 (mmp) cc_final: 0.7909 (mmp) REVERT: E 14 LYS cc_start: 0.9169 (ttmt) cc_final: 0.8836 (tttm) REVERT: E 24 THR cc_start: 0.7833 (m) cc_final: 0.7501 (p) REVERT: E 31 PHE cc_start: 0.9259 (m-80) cc_final: 0.8966 (m-80) REVERT: E 41 ASP cc_start: 0.7284 (m-30) cc_final: 0.6512 (m-30) REVERT: E 65 GLU cc_start: 0.8438 (pt0) cc_final: 0.8056 (pt0) REVERT: E 71 MET cc_start: 0.8049 (mtp) cc_final: 0.6800 (mtp) REVERT: F 9 MET cc_start: 0.8805 (tpp) cc_final: 0.8470 (tpp) REVERT: F 72 ASP cc_start: 0.9183 (m-30) cc_final: 0.8876 (m-30) REVERT: F 75 GLU cc_start: 0.9114 (pp20) cc_final: 0.8854 (pp20) REVERT: F 88 MET cc_start: 0.8473 (tmm) cc_final: 0.7716 (tmm) REVERT: F 90 MET cc_start: 0.8255 (mtp) cc_final: 0.7709 (tpp) REVERT: F 102 MET cc_start: 0.9323 (mpp) cc_final: 0.8929 (mpp) REVERT: H 10 MET cc_start: 0.9522 (tmm) cc_final: 0.9169 (ppp) REVERT: H 11 LEU cc_start: 0.9649 (mt) cc_final: 0.9378 (mt) REVERT: H 27 MET cc_start: 0.8601 (pmm) cc_final: 0.8377 (pmm) REVERT: H 86 TYR cc_start: 0.8545 (m-80) cc_final: 0.8074 (m-80) REVERT: H 107 SER cc_start: 0.9502 (m) cc_final: 0.8902 (t) REVERT: H 113 ASP cc_start: 0.9131 (p0) cc_final: 0.8735 (p0) REVERT: L 38 TYR cc_start: 0.9314 (p90) cc_final: 0.9085 (p90) REVERT: L 73 ASN cc_start: 0.9227 (m-40) cc_final: 0.8948 (p0) REVERT: L 112 GLN cc_start: 0.9052 (mm-40) cc_final: 0.8622 (mp10) REVERT: O 68 ASP cc_start: 0.9521 (m-30) cc_final: 0.9277 (m-30) REVERT: Q 11 ARG cc_start: 0.8458 (ttp80) cc_final: 0.8244 (ttp80) REVERT: Q 15 ASP cc_start: 0.8867 (p0) cc_final: 0.8571 (p0) REVERT: Q 17 MET cc_start: 0.8616 (mpp) cc_final: 0.8153 (mpp) REVERT: Q 25 ILE cc_start: 0.9104 (mp) cc_final: 0.8836 (mp) REVERT: Q 27 ARG cc_start: 0.9015 (ptt-90) cc_final: 0.8652 (ptt-90) REVERT: Q 42 THR cc_start: 0.8523 (p) cc_final: 0.7805 (p) REVERT: Q 55 ILE cc_start: 0.8654 (pt) cc_final: 0.8106 (mp) REVERT: R 61 ARG cc_start: 0.8831 (mtt180) cc_final: 0.8460 (mpt180) REVERT: T 28 MET cc_start: 0.9051 (tpp) cc_final: 0.8724 (tpt) REVERT: T 51 PHE cc_start: 0.9250 (t80) cc_final: 0.8959 (t80) REVERT: V 16 GLN cc_start: 0.8989 (mt0) cc_final: 0.8538 (pt0) REVERT: V 35 MET cc_start: 0.8754 (ppp) cc_final: 0.8458 (ppp) REVERT: X 1 MET cc_start: 0.0425 (mtt) cc_final: -0.0227 (mtt) REVERT: X 37 ARG cc_start: 0.9293 (mpp80) cc_final: 0.8840 (mtm-85) REVERT: X 109 ASN cc_start: 0.8597 (p0) cc_final: 0.8117 (p0) outliers start: 0 outliers final: 0 residues processed: 276 average time/residue: 0.5121 time to fit residues: 221.9532 Evaluate side-chains 213 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 230 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 174 optimal weight: 0.0570 chunk 135 optimal weight: 6.9990 chunk 201 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 238 optimal weight: 0.8980 chunk 148 optimal weight: 0.1980 chunk 145 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 overall best weight: 2.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.4368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 37175 Z= 0.149 Angle : 0.542 11.851 55443 Z= 0.283 Chirality : 0.031 0.238 7054 Planarity : 0.004 0.115 3113 Dihedral : 24.380 178.784 18122 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 24.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % 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: -0.92 (0.21), residues: 1458 helix: -0.01 (0.22), residues: 536 sheet: -1.06 (0.29), residues: 301 loop : -0.74 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 113 HIS 0.006 0.001 HIS X 56 PHE 0.023 0.002 PHE F 78 TYR 0.015 0.001 TYR L 95 ARG 0.013 0.001 ARG V 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 GLN cc_start: 0.9276 (mt0) cc_final: 0.9035 (mt0) REVERT: D 71 GLN cc_start: 0.8837 (tt0) cc_final: 0.8155 (tp-100) REVERT: D 72 PHE cc_start: 0.9602 (t80) cc_final: 0.8857 (t80) REVERT: D 75 TYR cc_start: 0.8720 (m-10) cc_final: 0.7735 (m-80) REVERT: D 124 MET cc_start: 0.8175 (mmp) cc_final: 0.7866 (mmp) REVERT: E 14 LYS cc_start: 0.9196 (ttmt) cc_final: 0.8852 (tttm) REVERT: E 24 THR cc_start: 0.7722 (m) cc_final: 0.7402 (p) REVERT: E 31 PHE cc_start: 0.9353 (m-80) cc_final: 0.9151 (m-80) REVERT: E 41 ASP cc_start: 0.7239 (m-30) cc_final: 0.6381 (m-30) REVERT: E 65 GLU cc_start: 0.8409 (pt0) cc_final: 0.7998 (pt0) REVERT: E 71 MET cc_start: 0.7979 (mtp) cc_final: 0.6690 (mtp) REVERT: E 86 LYS cc_start: 0.8617 (tptp) cc_final: 0.8363 (tptt) REVERT: E 112 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8444 (tpp80) REVERT: F 72 ASP cc_start: 0.9231 (m-30) cc_final: 0.8882 (m-30) REVERT: F 75 GLU cc_start: 0.9078 (pp20) cc_final: 0.8820 (pp20) REVERT: F 88 MET cc_start: 0.8353 (tmm) cc_final: 0.7899 (tmm) REVERT: F 102 MET cc_start: 0.9331 (mpp) cc_final: 0.9113 (mpp) REVERT: H 10 MET cc_start: 0.9519 (tmm) cc_final: 0.9214 (ppp) REVERT: H 11 LEU cc_start: 0.9640 (mt) cc_final: 0.9415 (mt) REVERT: H 27 MET cc_start: 0.8630 (pmm) cc_final: 0.8419 (pmm) REVERT: H 80 ARG cc_start: 0.8620 (mtp-110) cc_final: 0.8349 (mtp-110) REVERT: H 86 TYR cc_start: 0.8427 (m-80) cc_final: 0.7953 (m-80) REVERT: H 107 SER cc_start: 0.9463 (m) cc_final: 0.8759 (t) REVERT: H 113 ASP cc_start: 0.9094 (p0) cc_final: 0.8723 (p0) REVERT: L 38 TYR cc_start: 0.9288 (p90) cc_final: 0.8827 (p90) REVERT: L 73 ASN cc_start: 0.9243 (m-40) cc_final: 0.9019 (p0) REVERT: L 112 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8637 (mp10) REVERT: O 68 ASP cc_start: 0.9488 (m-30) cc_final: 0.9236 (m-30) REVERT: O 73 LYS cc_start: 0.9065 (mmmt) cc_final: 0.8550 (mtmt) REVERT: P 17 TYR cc_start: 0.8264 (m-80) cc_final: 0.7749 (m-80) REVERT: P 56 ARG cc_start: 0.9431 (tpm170) cc_final: 0.9092 (mmm160) REVERT: P 76 LYS cc_start: 0.9618 (tmtt) cc_final: 0.9409 (tmtt) REVERT: Q 11 ARG cc_start: 0.8464 (ttp80) cc_final: 0.8238 (ttp80) REVERT: Q 15 ASP cc_start: 0.8796 (p0) cc_final: 0.8509 (p0) REVERT: Q 17 MET cc_start: 0.8609 (mpp) cc_final: 0.8331 (mpp) REVERT: Q 25 ILE cc_start: 0.9125 (mp) cc_final: 0.8628 (mp) REVERT: Q 27 ARG cc_start: 0.9005 (ptt-90) cc_final: 0.8510 (ptt-90) REVERT: Q 42 THR cc_start: 0.8584 (p) cc_final: 0.6829 (p) REVERT: Q 55 ILE cc_start: 0.8628 (pt) cc_final: 0.8120 (mp) REVERT: V 47 LEU cc_start: 0.9073 (mm) cc_final: 0.8738 (tt) REVERT: X 1 MET cc_start: 0.0367 (mtt) cc_final: -0.0137 (mtt) REVERT: X 37 ARG cc_start: 0.9257 (mpp80) cc_final: 0.8838 (mtm-85) REVERT: X 93 ARG cc_start: 0.9092 (mtm180) cc_final: 0.8786 (mtm180) REVERT: X 109 ASN cc_start: 0.8741 (p0) cc_final: 0.8281 (p0) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.5245 time to fit residues: 237.8756 Evaluate side-chains 225 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 147 optimal weight: 0.5980 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 71 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 151 optimal weight: 10.0000 chunk 162 optimal weight: 30.0000 chunk 117 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 216 optimal weight: 1.9990 overall best weight: 4.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 ASN T 61 GLN ** V 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 37175 Z= 0.237 Angle : 0.581 11.768 55443 Z= 0.303 Chirality : 0.033 0.242 7054 Planarity : 0.005 0.116 3113 Dihedral : 24.359 179.589 18122 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 30.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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: -0.85 (0.22), residues: 1458 helix: 0.00 (0.22), residues: 533 sheet: -1.02 (0.30), residues: 286 loop : -0.67 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP X 113 HIS 0.008 0.002 HIS F 58 PHE 0.021 0.002 PHE V 98 TYR 0.015 0.002 TYR L 95 ARG 0.007 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLN cc_start: 0.8858 (tt0) cc_final: 0.8082 (tp-100) REVERT: D 72 PHE cc_start: 0.9632 (t80) cc_final: 0.8753 (t80) REVERT: D 75 TYR cc_start: 0.8758 (m-10) cc_final: 0.7727 (m-80) REVERT: D 103 TYR cc_start: 0.8505 (t80) cc_final: 0.8302 (t80) REVERT: D 124 MET cc_start: 0.8240 (mmp) cc_final: 0.7950 (mmp) REVERT: E 14 LYS cc_start: 0.9199 (ttmt) cc_final: 0.8874 (tttm) REVERT: E 24 THR cc_start: 0.7603 (m) cc_final: 0.7251 (p) REVERT: E 31 PHE cc_start: 0.9354 (m-80) cc_final: 0.8952 (m-80) REVERT: E 41 ASP cc_start: 0.7283 (m-30) cc_final: 0.6696 (m-30) REVERT: E 65 GLU cc_start: 0.8352 (pt0) cc_final: 0.7938 (pt0) REVERT: E 71 MET cc_start: 0.8112 (mtp) cc_final: 0.6920 (mtp) REVERT: E 86 LYS cc_start: 0.8601 (tptp) cc_final: 0.8387 (tptt) REVERT: F 9 MET cc_start: 0.8748 (tpp) cc_final: 0.8452 (tpp) REVERT: F 72 ASP cc_start: 0.9257 (m-30) cc_final: 0.8902 (m-30) REVERT: F 75 GLU cc_start: 0.9096 (pp20) cc_final: 0.8834 (pp20) REVERT: F 88 MET cc_start: 0.8385 (tmm) cc_final: 0.7510 (tmm) REVERT: F 102 MET cc_start: 0.9378 (mpp) cc_final: 0.9060 (mpp) REVERT: H 10 MET cc_start: 0.9521 (tmm) cc_final: 0.9236 (ppp) REVERT: H 11 LEU cc_start: 0.9658 (mt) cc_final: 0.9433 (mt) REVERT: H 107 SER cc_start: 0.9473 (m) cc_final: 0.8820 (t) REVERT: H 113 ASP cc_start: 0.9091 (p0) cc_final: 0.8659 (p0) REVERT: L 38 TYR cc_start: 0.9305 (p90) cc_final: 0.9015 (p90) REVERT: L 73 ASN cc_start: 0.9227 (m-40) cc_final: 0.9001 (p0) REVERT: L 112 GLN cc_start: 0.9055 (mm-40) cc_final: 0.8621 (mp10) REVERT: O 68 ASP cc_start: 0.9497 (m-30) cc_final: 0.9257 (m-30) REVERT: P 17 TYR cc_start: 0.8302 (m-80) cc_final: 0.7813 (m-80) REVERT: Q 15 ASP cc_start: 0.8844 (p0) cc_final: 0.8498 (p0) REVERT: Q 17 MET cc_start: 0.8613 (mpp) cc_final: 0.8248 (mpp) REVERT: Q 27 ARG cc_start: 0.9041 (ptt-90) cc_final: 0.8553 (ptt-90) REVERT: Q 42 THR cc_start: 0.8543 (p) cc_final: 0.6960 (p) REVERT: Q 55 ILE cc_start: 0.8634 (pt) cc_final: 0.8103 (mp) REVERT: T 79 LEU cc_start: 0.9279 (mt) cc_final: 0.9062 (mt) REVERT: V 51 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8690 (mmmm) REVERT: X 1 MET cc_start: 0.0072 (mtt) cc_final: -0.0513 (mtt) REVERT: X 37 ARG cc_start: 0.9296 (mpp80) cc_final: 0.8805 (mtm-85) REVERT: X 93 ARG cc_start: 0.9130 (mtm180) cc_final: 0.8901 (mtm180) REVERT: X 109 ASN cc_start: 0.8742 (p0) cc_final: 0.8363 (p0) outliers start: 0 outliers final: 0 residues processed: 273 average time/residue: 0.5319 time to fit residues: 228.2171 Evaluate side-chains 218 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 228 optimal weight: 20.0000 chunk 208 optimal weight: 8.9990 chunk 221 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 96 optimal weight: 20.0000 chunk 174 optimal weight: 9.9990 chunk 68 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 209 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 234 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 37175 Z= 0.353 Angle : 0.678 11.719 55443 Z= 0.349 Chirality : 0.037 0.249 7054 Planarity : 0.005 0.118 3113 Dihedral : 24.512 179.858 18122 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 38.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -1.13 (0.21), residues: 1458 helix: -0.27 (0.21), residues: 532 sheet: -1.17 (0.29), residues: 291 loop : -0.78 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP X 113 HIS 0.011 0.002 HIS F 58 PHE 0.028 0.003 PHE V 98 TYR 0.020 0.002 TYR D 103 ARG 0.011 0.001 ARG V 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 GLU cc_start: 0.9142 (tp30) cc_final: 0.8929 (tp30) REVERT: D 71 GLN cc_start: 0.8895 (tt0) cc_final: 0.8160 (tp-100) REVERT: D 72 PHE cc_start: 0.9635 (t80) cc_final: 0.8774 (t80) REVERT: D 75 TYR cc_start: 0.8777 (m-10) cc_final: 0.7745 (m-80) REVERT: D 103 TYR cc_start: 0.8706 (t80) cc_final: 0.8500 (t80) REVERT: D 124 MET cc_start: 0.8390 (mmp) cc_final: 0.8174 (mmp) REVERT: E 31 PHE cc_start: 0.9259 (m-80) cc_final: 0.8848 (m-80) REVERT: E 41 ASP cc_start: 0.7219 (m-30) cc_final: 0.6359 (m-30) REVERT: E 65 GLU cc_start: 0.8319 (pt0) cc_final: 0.7911 (pt0) REVERT: E 71 MET cc_start: 0.8193 (mtp) cc_final: 0.6953 (mtp) REVERT: E 88 VAL cc_start: 0.8614 (t) cc_final: 0.7043 (t) REVERT: F 9 MET cc_start: 0.8874 (tpp) cc_final: 0.8546 (tpp) REVERT: F 72 ASP cc_start: 0.9326 (m-30) cc_final: 0.8961 (m-30) REVERT: F 75 GLU cc_start: 0.9129 (pp20) cc_final: 0.8870 (pp20) REVERT: F 88 MET cc_start: 0.8685 (tmm) cc_final: 0.8157 (tmm) REVERT: F 102 MET cc_start: 0.9425 (mpp) cc_final: 0.9060 (mpp) REVERT: H 10 MET cc_start: 0.9550 (tmm) cc_final: 0.9214 (tmm) REVERT: H 11 LEU cc_start: 0.9685 (mt) cc_final: 0.9290 (mt) REVERT: H 86 TYR cc_start: 0.8430 (m-80) cc_final: 0.7963 (m-80) REVERT: H 99 LEU cc_start: 0.9398 (mt) cc_final: 0.9194 (mt) REVERT: H 107 SER cc_start: 0.9455 (m) cc_final: 0.8824 (t) REVERT: H 113 ASP cc_start: 0.9182 (p0) cc_final: 0.8772 (p0) REVERT: L 38 TYR cc_start: 0.9345 (p90) cc_final: 0.8647 (p90) REVERT: L 73 ASN cc_start: 0.9288 (m-40) cc_final: 0.9064 (p0) REVERT: L 112 GLN cc_start: 0.9095 (mm-40) cc_final: 0.8665 (mp10) REVERT: O 68 ASP cc_start: 0.9535 (m-30) cc_final: 0.9321 (m-30) REVERT: Q 15 ASP cc_start: 0.8836 (p0) cc_final: 0.8600 (p0) REVERT: Q 17 MET cc_start: 0.8562 (mpp) cc_final: 0.8224 (mpp) REVERT: Q 25 ILE cc_start: 0.8999 (mp) cc_final: 0.8477 (mp) REVERT: Q 27 ARG cc_start: 0.9068 (ptt-90) cc_final: 0.8583 (ptt-90) REVERT: Q 42 THR cc_start: 0.8424 (p) cc_final: 0.6888 (p) REVERT: Q 55 ILE cc_start: 0.8559 (pt) cc_final: 0.8322 (pt) REVERT: T 54 MET cc_start: 0.8697 (tmm) cc_final: 0.8493 (tmm) REVERT: T 79 LEU cc_start: 0.9339 (mt) cc_final: 0.9138 (mt) REVERT: V 51 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8766 (mmmm) REVERT: V 66 LYS cc_start: 0.9111 (ptpp) cc_final: 0.8849 (pttt) REVERT: X 1 MET cc_start: -0.0229 (mtt) cc_final: -0.0719 (mtt) REVERT: X 37 ARG cc_start: 0.9334 (mpp80) cc_final: 0.8826 (mtm-85) REVERT: X 109 ASN cc_start: 0.8748 (p0) cc_final: 0.8526 (p0) outliers start: 0 outliers final: 0 residues processed: 258 average time/residue: 0.5089 time to fit residues: 206.3888 Evaluate side-chains 205 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 143 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 163 optimal weight: 6.9990 chunk 246 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 195 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 151 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 GLN ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 61 GLN ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37175 Z= 0.206 Angle : 0.584 11.815 55443 Z= 0.305 Chirality : 0.033 0.244 7054 Planarity : 0.005 0.115 3113 Dihedral : 24.467 178.698 18122 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 29.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: -1.11 (0.21), residues: 1458 helix: -0.14 (0.21), residues: 532 sheet: -1.23 (0.29), residues: 298 loop : -0.83 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 113 HIS 0.007 0.001 HIS X 56 PHE 0.020 0.002 PHE F 78 TYR 0.016 0.002 TYR L 95 ARG 0.008 0.001 ARG F 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2916 Ramachandran restraints generated. 1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 71 GLN cc_start: 0.8842 (tt0) cc_final: 0.8159 (tp-100) REVERT: D 72 PHE cc_start: 0.9622 (t80) cc_final: 0.8863 (t80) REVERT: D 75 TYR cc_start: 0.8735 (m-10) cc_final: 0.7767 (m-80) REVERT: D 124 MET cc_start: 0.8243 (mmp) cc_final: 0.7977 (mmp) REVERT: E 31 PHE cc_start: 0.9223 (m-80) cc_final: 0.8922 (m-80) REVERT: E 41 ASP cc_start: 0.7265 (m-30) cc_final: 0.6687 (m-30) REVERT: E 65 GLU cc_start: 0.8372 (pt0) cc_final: 0.7909 (pt0) REVERT: E 71 MET cc_start: 0.8189 (mtp) cc_final: 0.6960 (mtp) REVERT: F 9 MET cc_start: 0.8885 (tpp) cc_final: 0.8550 (tpp) REVERT: F 72 ASP cc_start: 0.9276 (m-30) cc_final: 0.8902 (m-30) REVERT: F 75 GLU cc_start: 0.9097 (pp20) cc_final: 0.8842 (pp20) REVERT: F 88 MET cc_start: 0.8283 (tmm) cc_final: 0.7944 (tmm) REVERT: H 10 MET cc_start: 0.9551 (tmm) cc_final: 0.9215 (tmm) REVERT: H 11 LEU cc_start: 0.9666 (mt) cc_final: 0.9289 (mt) REVERT: H 107 SER cc_start: 0.9460 (m) cc_final: 0.8814 (t) REVERT: H 113 ASP cc_start: 0.9101 (p0) cc_final: 0.8659 (p0) REVERT: H 121 LEU cc_start: 0.9450 (mt) cc_final: 0.9096 (tt) REVERT: L 38 TYR cc_start: 0.9327 (p90) cc_final: 0.8605 (p90) REVERT: L 73 ASN cc_start: 0.9284 (m-40) cc_final: 0.9018 (p0) REVERT: L 112 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8626 (mp10) REVERT: O 68 ASP cc_start: 0.9519 (m-30) cc_final: 0.9300 (m-30) REVERT: P 17 TYR cc_start: 0.8396 (m-80) cc_final: 0.7801 (m-80) REVERT: Q 15 ASP cc_start: 0.8808 (p0) cc_final: 0.8459 (p0) REVERT: Q 17 MET cc_start: 0.8578 (mpp) cc_final: 0.8227 (mpp) REVERT: Q 25 ILE cc_start: 0.9080 (mp) cc_final: 0.8554 (mp) REVERT: Q 27 ARG cc_start: 0.9050 (ptt-90) cc_final: 0.8584 (ptt-90) REVERT: Q 42 THR cc_start: 0.8477 (p) cc_final: 0.6848 (p) REVERT: Q 55 ILE cc_start: 0.8640 (pt) cc_final: 0.8065 (mp) REVERT: R 29 LEU cc_start: 0.9353 (mm) cc_final: 0.9145 (mm) REVERT: X 1 MET cc_start: -0.0332 (mtt) cc_final: -0.0848 (mtt) REVERT: X 37 ARG cc_start: 0.9318 (mpp80) cc_final: 0.8795 (mtm-85) REVERT: X 93 ARG cc_start: 0.9070 (mtm180) cc_final: 0.8773 (mtm180) REVERT: X 109 ASN cc_start: 0.8838 (p0) cc_final: 0.8610 (p0) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.5155 time to fit residues: 215.4879 Evaluate side-chains 214 residues out of total 1229 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 247 random chunks: chunk 60 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 196 optimal weight: 20.0000 chunk 82 optimal weight: 20.0000 chunk 201 optimal weight: 0.0980 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 172 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 overall best weight: 7.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 70 ASN ** F 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.024301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.020015 restraints weight = 526375.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.020761 restraints weight = 224031.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.021216 restraints weight = 129392.894| |-----------------------------------------------------------------------------| r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 37175 Z= 0.311 Angle : 0.649 11.736 55443 Z= 0.336 Chirality : 0.036 0.253 7054 Planarity : 0.005 0.117 3113 Dihedral : 24.521 179.428 18122 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 37.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -1.32 (0.21), residues: 1458 helix: -0.37 (0.21), residues: 533 sheet: -1.32 (0.28), residues: 310 loop : -0.89 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP X 113 HIS 0.009 0.002 HIS F 58 PHE 0.023 0.003 PHE V 98 TYR 0.019 0.002 TYR D 103 ARG 0.009 0.001 ARG V 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5608.23 seconds wall clock time: 105 minutes 49.02 seconds (6349.02 seconds total)