Starting phenix.real_space_refine on Mon Mar 11 19:05:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/03_2024/8i0q_35106_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/03_2024/8i0q_35106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/03_2024/8i0q_35106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/03_2024/8i0q_35106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/03_2024/8i0q_35106_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i0q_35106/03_2024/8i0q_35106_updated.pdb" } resolution = 4.45 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= 0.019 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 30 5.16 5 C 5601 2.51 5 N 1489 2.21 5 O 1712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8842 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2683 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334} Unresolved non-hydrogen bonds: 194 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 14, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 2679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2679 Classifications: {'peptide': 363} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 334} Unresolved non-hydrogen bonds: 198 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 15, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 134 Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 892 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 893 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 769 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 773 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "U" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 79 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "V" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 74 Classifications: {'peptide': 9} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 8} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.26, per 1000 atoms: 0.59 Number of scatterers: 8842 At special positions: 0 Unit cell: (130.058, 153.106, 85.6076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 10 15.00 O 1712 8.00 N 1489 7.00 C 5601 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 25 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 24 " - pdb=" SG CYS M 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2232 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 17 helices and 22 sheets defined 5.5% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 336 through 338 No H-bonds generated for 'chain 'B' and resid 336 through 338' Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'I' and resid 65 through 67 No H-bonds generated for 'chain 'I' and resid 65 through 67' Processing helix chain 'I' and resid 91 through 93 No H-bonds generated for 'chain 'I' and resid 91 through 93' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'M' and resid 81 through 83 No H-bonds generated for 'chain 'M' and resid 81 through 83' Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.525A pdb=" N LEU A 22 " --> pdb=" O PHE A 9 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 21 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL A 40 " --> pdb=" O TYR A 21 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.236A pdb=" N ARG A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 80 through 84 removed outlier: 3.624A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG A 62 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 61 through 64 removed outlier: 3.704A pdb=" N TYR A 63 " --> pdb=" O PHE A 75 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= F, first strand: chain 'A' and resid 183 through 188 Processing sheet with id= G, first strand: chain 'A' and resid 343 through 349 removed outlier: 4.446A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA A 254 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE A 241 " --> pdb=" O GLN A 248 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N GLN A 248 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 9 through 12 removed outlier: 3.565A pdb=" N TYR B 21 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL B 40 " --> pdb=" O TYR B 21 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 26 through 29 removed outlier: 6.235A pdb=" N ARG B 169 " --> pdb=" O PHE B 27 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP B 29 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL B 171 " --> pdb=" O ASP B 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 74 through 77 removed outlier: 3.602A pdb=" N TYR B 63 " --> pdb=" O PHE B 75 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 60 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASP B 143 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG B 62 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 183 through 188 Processing sheet with id= L, first strand: chain 'B' and resid 343 through 349 removed outlier: 4.496A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 254 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 8 through 10 removed outlier: 3.895A pdb=" N LEU H 23 " --> pdb=" O LEU H 84 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 96 through 103 removed outlier: 3.542A pdb=" N VAL H 40 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA H 100 " --> pdb=" O HIS H 38 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE H 37 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR H 62 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR H 60 " --> pdb=" O SER H 55 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'I' and resid 8 through 10 removed outlier: 3.852A pdb=" N LEU I 23 " --> pdb=" O LEU I 84 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR I 81 " --> pdb=" O ASP I 76 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 96 through 103 removed outlier: 3.590A pdb=" N VAL I 40 " --> pdb=" O TYR I 98 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA I 100 " --> pdb=" O HIS I 38 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS I 38 " --> pdb=" O ALA I 100 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA I 52 " --> pdb=" O TRP I 39 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ARG I 41 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N TRP I 50 " --> pdb=" O ARG I 41 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR I 62 " --> pdb=" O SER I 53 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'L' and resid 6 through 8 removed outlier: 3.537A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 11 through 13 removed outlier: 7.131A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'L' and resid 86 through 91 removed outlier: 6.005A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'M' and resid 5 through 8 removed outlier: 3.519A pdb=" N VAL M 20 " --> pdb=" O ILE M 76 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 11 through 13 removed outlier: 7.197A pdb=" N LYS M 104 " --> pdb=" O LEU M 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'M' and resid 86 through 91 removed outlier: 6.053A pdb=" N GLN M 38 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LEU M 47 " --> pdb=" O GLN M 38 " (cutoff:3.500A) 253 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2858 1.34 - 1.46: 2084 1.46 - 1.58: 4026 1.58 - 1.69: 37 1.69 - 1.81: 38 Bond restraints: 9043 Sorted by residual: bond pdb=" O2P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.514 0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O3P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.515 0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" O1P SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 1.610 1.516 0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" C MET B 352 " pdb=" N HIS B 353 " ideal model delta sigma weight residual 1.331 1.381 -0.050 2.83e-02 1.25e+03 3.06e+00 bond pdb=" C MET A 352 " pdb=" N HIS A 353 " ideal model delta sigma weight residual 1.331 1.380 -0.049 2.83e-02 1.25e+03 3.03e+00 ... (remaining 9038 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.33: 371 107.33 - 114.00: 5161 114.00 - 120.67: 3142 120.67 - 127.34: 3592 127.34 - 134.01: 107 Bond angle restraints: 12373 Sorted by residual: angle pdb=" C GLU B 308 " pdb=" CA GLU B 308 " pdb=" CB GLU B 308 " ideal model delta sigma weight residual 115.79 110.62 5.17 1.19e+00 7.06e-01 1.89e+01 angle pdb=" N ARG A 103 " pdb=" CA ARG A 103 " pdb=" C ARG A 103 " ideal model delta sigma weight residual 111.02 106.97 4.05 1.22e+00 6.72e-01 1.10e+01 angle pdb=" CB SEP V 351 " pdb=" OG SEP V 351 " pdb=" P SEP V 351 " ideal model delta sigma weight residual 110.00 118.39 -8.39 3.00e+00 1.11e-01 7.83e+00 angle pdb=" O ARG A 103 " pdb=" C ARG A 103 " pdb=" N LEU A 104 " ideal model delta sigma weight residual 122.08 124.67 -2.59 1.07e+00 8.73e-01 5.84e+00 angle pdb=" N PHE B 149 " pdb=" CA PHE B 149 " pdb=" C PHE B 149 " ideal model delta sigma weight residual 107.73 110.83 -3.10 1.34e+00 5.57e-01 5.36e+00 ... (remaining 12368 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 4986 16.96 - 33.91: 334 33.91 - 50.87: 52 50.87 - 67.83: 11 67.83 - 84.79: 12 Dihedral angle restraints: 5395 sinusoidal: 1923 harmonic: 3472 Sorted by residual: dihedral pdb=" CA GLN L 4 " pdb=" C GLN L 4 " pdb=" N MET L 5 " pdb=" CA MET L 5 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA PHE B 190 " pdb=" C PHE B 190 " pdb=" N LEU B 191 " pdb=" CA LEU B 191 " ideal model delta harmonic sigma weight residual 180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PHE A 190 " pdb=" C PHE A 190 " pdb=" N LEU A 191 " pdb=" CA LEU A 191 " ideal model delta harmonic sigma weight residual 180.00 -162.81 -17.19 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 877 0.029 - 0.058: 381 0.058 - 0.088: 52 0.088 - 0.117: 100 0.117 - 0.146: 26 Chirality restraints: 1436 Sorted by residual: chirality pdb=" CA ILE A 241 " pdb=" N ILE A 241 " pdb=" C ILE A 241 " pdb=" CB ILE A 241 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL A 343 " pdb=" N VAL A 343 " pdb=" C VAL A 343 " pdb=" CB VAL A 343 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL B 345 " pdb=" N VAL B 345 " pdb=" C VAL B 345 " pdb=" CB VAL B 345 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 1433 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 275 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO B 276 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 276 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 276 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 275 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 276 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN I 16 " 0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO I 17 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO I 17 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 17 " 0.018 5.00e-02 4.00e+02 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 570 2.71 - 3.26: 9462 3.26 - 3.81: 14099 3.81 - 4.35: 16650 4.35 - 4.90: 27919 Nonbonded interactions: 68700 Sorted by model distance: nonbonded pdb=" NE2 GLN B 172 " pdb=" O TYR B 173 " model vdw 2.167 2.520 nonbonded pdb=" NZ LYS A 107 " pdb=" O1P SEP V 347 " model vdw 2.203 2.520 nonbonded pdb=" O GLN I 6 " pdb=" OG SER I 28 " model vdw 2.226 2.440 nonbonded pdb=" ND2 ASN A 222 " pdb=" O ALA A 263 " model vdw 2.229 2.520 nonbonded pdb=" NE ARG B 62 " pdb=" OG1 THR B 74 " model vdw 2.236 2.520 ... (remaining 68695 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 133 or (resid 134 and (name N or name CA or name \ C or name O or name CB )) or resid 135 through 368)) selection = chain 'B' } ncs_group { reference = chain 'H' selection = (chain 'I' and (resid 5 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB )) or resid 29 through 122)) } ncs_group { reference = chain 'L' selection = (chain 'M' and (resid 1 through 90 or (resid 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 106)) } ncs_group { reference = (chain 'U' and (resid 343 through 349 or (resid 350 and (name N or name CA or na \ me C or name O or name CB )) or resid 351)) selection = chain 'V' } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.100 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.440 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 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 : 0.003 0.096 9043 Z= 0.215 Angle : 0.593 8.393 12373 Z= 0.329 Chirality : 0.043 0.146 1436 Planarity : 0.004 0.047 1587 Dihedral : 12.560 84.785 3151 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.41 (0.25), residues: 1162 helix: -1.43 (1.04), residues: 22 sheet: -1.01 (0.23), residues: 464 loop : -0.79 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 106 HIS 0.004 0.001 HIS B 210 PHE 0.009 0.001 PHE L 72 TYR 0.008 0.001 TYR B 113 ARG 0.006 0.000 ARG H 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 7 LEU cc_start: 0.6995 (pt) cc_final: 0.6702 (pp) REVERT: H 21 LEU cc_start: 0.9417 (mt) cc_final: 0.9197 (mp) REVERT: H 86 MET cc_start: 0.7768 (pmm) cc_final: 0.7361 (pmm) REVERT: I 7 LEU cc_start: 0.7424 (pt) cc_final: 0.7080 (pp) REVERT: I 21 LEU cc_start: 0.9413 (mt) cc_final: 0.9194 (mp) REVERT: I 86 MET cc_start: 0.7567 (pmm) cc_final: 0.7110 (pmm) REVERT: L 5 MET cc_start: 0.7409 (ttt) cc_final: 0.6658 (pmm) REVERT: L 101 GLN cc_start: 0.8947 (mp10) cc_final: 0.8647 (pm20) REVERT: M 5 MET cc_start: 0.7713 (ttp) cc_final: 0.6691 (pmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1562 time to fit residues: 10.6953 Evaluate side-chains 29 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 219 HIS ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9043 Z= 0.262 Angle : 0.637 5.603 12373 Z= 0.333 Chirality : 0.044 0.175 1436 Planarity : 0.004 0.034 1587 Dihedral : 8.205 88.612 1314 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.28 (0.25), residues: 1162 helix: -1.57 (0.96), residues: 22 sheet: -0.97 (0.23), residues: 474 loop : -0.63 (0.26), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 39 HIS 0.008 0.002 HIS B 210 PHE 0.019 0.003 PHE B 190 TYR 0.018 0.002 TYR I 107 ARG 0.005 0.001 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 CYS cc_start: 0.7996 (p) cc_final: 0.7609 (p) REVERT: A 352 MET cc_start: 0.9055 (ptm) cc_final: 0.8192 (ptm) REVERT: B 150 CYS cc_start: 0.8207 (p) cc_final: 0.7724 (p) REVERT: I 21 LEU cc_start: 0.9659 (mt) cc_final: 0.9340 (tp) REVERT: I 86 MET cc_start: 0.7871 (pmm) cc_final: 0.7486 (pmm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1364 time to fit residues: 8.5443 Evaluate side-chains 25 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 92 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9043 Z= 0.220 Angle : 0.594 7.166 12373 Z= 0.306 Chirality : 0.043 0.163 1436 Planarity : 0.004 0.051 1587 Dihedral : 8.094 89.226 1314 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.14 (0.25), residues: 1162 helix: -1.37 (0.99), residues: 22 sheet: -0.83 (0.22), residues: 488 loop : -0.57 (0.26), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 39 HIS 0.005 0.002 HIS B 210 PHE 0.015 0.002 PHE A 190 TYR 0.016 0.001 TYR I 107 ARG 0.003 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.997 Fit side-chains revert: symmetry clash REVERT: A 150 CYS cc_start: 0.7844 (p) cc_final: 0.7524 (p) REVERT: A 352 MET cc_start: 0.8779 (ptm) cc_final: 0.7753 (ptm) REVERT: B 150 CYS cc_start: 0.7770 (p) cc_final: 0.7421 (p) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1490 time to fit residues: 9.2332 Evaluate side-chains 22 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.0170 chunk 77 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 11 optimal weight: 0.0980 chunk 49 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 0.0470 chunk 29 optimal weight: 10.0000 overall best weight: 2.2320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9043 Z= 0.255 Angle : 0.614 6.671 12373 Z= 0.318 Chirality : 0.043 0.161 1436 Planarity : 0.004 0.042 1587 Dihedral : 8.171 88.806 1314 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.21 (0.25), residues: 1162 helix: -1.57 (0.97), residues: 22 sheet: -0.92 (0.22), residues: 478 loop : -0.58 (0.26), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 39 HIS 0.007 0.002 HIS B 210 PHE 0.016 0.002 PHE B 190 TYR 0.019 0.001 TYR I 107 ARG 0.004 0.001 ARG I 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 1.071 Fit side-chains REVERT: A 150 CYS cc_start: 0.7929 (p) cc_final: 0.7531 (p) REVERT: A 352 MET cc_start: 0.8715 (ptm) cc_final: 0.7410 (ptm) REVERT: B 150 CYS cc_start: 0.7740 (p) cc_final: 0.7372 (p) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1365 time to fit residues: 7.9758 Evaluate side-chains 22 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 76 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9043 Z= 0.282 Angle : 0.642 5.693 12373 Z= 0.332 Chirality : 0.043 0.174 1436 Planarity : 0.004 0.037 1587 Dihedral : 8.263 89.832 1314 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.39 (0.25), residues: 1162 helix: -1.86 (0.93), residues: 22 sheet: -1.02 (0.22), residues: 482 loop : -0.70 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 39 HIS 0.007 0.002 HIS B 210 PHE 0.035 0.003 PHE I 105 TYR 0.022 0.002 TYR I 107 ARG 0.004 0.001 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 1.267 Fit side-chains REVERT: A 150 CYS cc_start: 0.8001 (p) cc_final: 0.7663 (p) REVERT: A 352 MET cc_start: 0.8673 (ptm) cc_final: 0.7454 (ptm) REVERT: B 150 CYS cc_start: 0.7778 (p) cc_final: 0.7445 (p) REVERT: B 352 MET cc_start: 0.9020 (ptm) cc_final: 0.8243 (ptm) REVERT: L 24 CYS cc_start: 0.2321 (t) cc_final: -0.0012 (t) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.1409 time to fit residues: 8.0748 Evaluate side-chains 24 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 0.7980 chunk 99 optimal weight: 0.0470 chunk 21 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9043 Z= 0.165 Angle : 0.555 5.174 12373 Z= 0.280 Chirality : 0.042 0.164 1436 Planarity : 0.004 0.031 1587 Dihedral : 7.741 88.781 1314 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.08 (0.25), residues: 1162 helix: -1.24 (1.07), residues: 22 sheet: -0.69 (0.23), residues: 462 loop : -0.64 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 36 HIS 0.003 0.001 HIS B 210 PHE 0.044 0.002 PHE H 105 TYR 0.009 0.001 TYR I 107 ARG 0.002 0.000 ARG M 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 1.079 Fit side-chains REVERT: A 150 CYS cc_start: 0.7738 (p) cc_final: 0.7382 (p) REVERT: A 352 MET cc_start: 0.8513 (ptm) cc_final: 0.7116 (ptm) REVERT: B 150 CYS cc_start: 0.7420 (p) cc_final: 0.7098 (p) REVERT: B 352 MET cc_start: 0.8895 (ptm) cc_final: 0.8431 (ptm) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1549 time to fit residues: 9.5129 Evaluate side-chains 24 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 92 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 109 optimal weight: 0.0570 chunk 68 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.9104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9043 Z= 0.315 Angle : 0.654 6.115 12373 Z= 0.340 Chirality : 0.043 0.175 1436 Planarity : 0.004 0.038 1587 Dihedral : 8.267 88.470 1314 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1162 helix: -1.79 (0.96), residues: 22 sheet: -0.87 (0.23), residues: 478 loop : -0.84 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 39 HIS 0.006 0.002 HIS A 219 PHE 0.018 0.003 PHE H 105 TYR 0.023 0.002 TYR I 107 ARG 0.005 0.001 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 1.088 Fit side-chains REVERT: A 150 CYS cc_start: 0.8091 (p) cc_final: 0.7730 (p) REVERT: A 352 MET cc_start: 0.8626 (ptm) cc_final: 0.7468 (ptm) REVERT: B 150 CYS cc_start: 0.7850 (p) cc_final: 0.7546 (p) REVERT: B 352 MET cc_start: 0.9167 (ptm) cc_final: 0.8599 (ptm) outliers start: 0 outliers final: 0 residues processed: 32 average time/residue: 0.1610 time to fit residues: 9.0599 Evaluate side-chains 23 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 33 optimal weight: 0.0980 chunk 21 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9043 Z= 0.324 Angle : 0.675 6.548 12373 Z= 0.353 Chirality : 0.044 0.198 1436 Planarity : 0.004 0.034 1587 Dihedral : 8.498 89.466 1314 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.86 % Favored : 91.05 % Rotamer: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.65 (0.24), residues: 1162 helix: -2.36 (0.83), residues: 22 sheet: -1.05 (0.22), residues: 482 loop : -1.01 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 39 HIS 0.006 0.002 HIS B 295 PHE 0.017 0.003 PHE A 149 TYR 0.022 0.002 TYR I 107 ARG 0.006 0.001 ARG A 363 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 33 time to evaluate : 1.182 Fit side-chains REVERT: A 150 CYS cc_start: 0.8148 (p) cc_final: 0.7822 (p) REVERT: A 352 MET cc_start: 0.8613 (ptm) cc_final: 0.7501 (ptm) REVERT: B 150 CYS cc_start: 0.7948 (p) cc_final: 0.7673 (p) REVERT: B 352 MET cc_start: 0.9203 (ptm) cc_final: 0.8657 (ptm) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.1495 time to fit residues: 9.3027 Evaluate side-chains 22 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 0.0270 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 66 optimal weight: 0.1980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9043 Z= 0.142 Angle : 0.548 5.177 12373 Z= 0.273 Chirality : 0.043 0.159 1436 Planarity : 0.003 0.029 1587 Dihedral : 7.629 88.620 1314 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.20 (0.25), residues: 1162 helix: -1.33 (1.08), residues: 22 sheet: -0.59 (0.24), residues: 432 loop : -0.88 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 36 HIS 0.002 0.001 HIS A 159 PHE 0.017 0.001 PHE H 105 TYR 0.008 0.001 TYR B 113 ARG 0.002 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.165 Fit side-chains REVERT: A 150 CYS cc_start: 0.7588 (p) cc_final: 0.7283 (p) REVERT: A 352 MET cc_start: 0.8833 (ptm) cc_final: 0.7574 (ptm) REVERT: B 150 CYS cc_start: 0.7366 (p) cc_final: 0.7112 (p) REVERT: B 352 MET cc_start: 0.8850 (ptm) cc_final: 0.8421 (ptm) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1586 time to fit residues: 10.6990 Evaluate side-chains 26 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9043 Z= 0.225 Angle : 0.573 5.311 12373 Z= 0.294 Chirality : 0.042 0.152 1436 Planarity : 0.004 0.031 1587 Dihedral : 7.815 88.976 1314 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.21 (0.25), residues: 1162 helix: -1.48 (1.06), residues: 22 sheet: -0.69 (0.23), residues: 480 loop : -0.80 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 39 HIS 0.005 0.001 HIS B 295 PHE 0.019 0.002 PHE L 84 TYR 0.015 0.001 TYR H 107 ARG 0.003 0.000 ARG B 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.095 Fit side-chains REVERT: A 150 CYS cc_start: 0.8061 (p) cc_final: 0.7758 (p) REVERT: A 352 MET cc_start: 0.8566 (ptm) cc_final: 0.7305 (ptm) REVERT: B 150 CYS cc_start: 0.7569 (p) cc_final: 0.7309 (p) REVERT: B 352 MET cc_start: 0.8967 (ptm) cc_final: 0.8557 (ptm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.1541 time to fit residues: 9.2810 Evaluate side-chains 25 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 0.4980 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN ** B 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 GLN ** 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 = 0.3003 r_free = 0.3003 target = 0.038035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.031170 restraints weight = 92885.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.032071 restraints weight = 58845.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.032718 restraints weight = 42791.750| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9043 Z= 0.198 Angle : 0.559 5.288 12373 Z= 0.285 Chirality : 0.042 0.154 1436 Planarity : 0.004 0.031 1587 Dihedral : 7.749 88.846 1314 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.18 % 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: -1.23 (0.25), residues: 1162 helix: -1.42 (1.07), residues: 22 sheet: -0.71 (0.23), residues: 490 loop : -0.81 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 39 HIS 0.004 0.001 HIS B 295 PHE 0.014 0.002 PHE A 149 TYR 0.013 0.001 TYR H 107 ARG 0.002 0.000 ARG L 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1603.82 seconds wall clock time: 30 minutes 20.41 seconds (1820.41 seconds total)