Starting phenix.real_space_refine on Sun Sep 29 09:04:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/09_2024/6zbb_11149_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/09_2024/6zbb_11149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/09_2024/6zbb_11149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/09_2024/6zbb_11149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/09_2024/6zbb_11149_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zbb_11149/09_2024/6zbb_11149_trim.cif" } resolution = 3.61 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= 0.001 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 8 5.49 5 S 55 5.16 5 C 6974 2.51 5 N 1617 2.21 5 O 1836 1.98 5 H 10592 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21082 Number of models: 1 Model: "" Number of chains: 20 Chain: "8" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 696 Classifications: {'peptide': 41} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "K" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 1078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1078 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "O" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1079 Classifications: {'peptide': 74} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 1095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1095 Classifications: {'peptide': 75} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M3L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3557 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 12, 'TRANS': 211} Chain: "b" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1791 Classifications: {'peptide': 112} Modifications used: {'NH2': 1} Link IDs: {'PTRANS': 7, 'TRANS': 104} Chain: "d" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 893 Classifications: {'peptide': 51} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 45} Chain: "e" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 975 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 3, 'TRANS': 53} Chain: "f" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1411 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain: "g" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 1291 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "j" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 828 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "k" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 596 Classifications: {'peptide': 36} Link IDs: {'TRANS': 35} Chain: "a" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 84 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Chain: "b" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 161 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "f" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 88 Unusual residues: {'LHG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Time building chain proxies: 11.14, per 1000 atoms: 0.53 Number of scatterers: 21082 At special positions: 0 Unit cell: (111.088, 125.76, 121.568, 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 55 16.00 P 8 15.00 O 1836 8.00 N 1617 7.00 C 6974 6.00 H 10592 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.10 Conformation dependent library (CDL) restraints added in 2.0 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 1 sheets defined 85.6% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain '8' and resid 1 through 7 removed outlier: 5.455A pdb=" N THR 8 6 " --> pdb=" O GLN 8 3 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N SER 8 7 " --> pdb=" O LEU 8 4 " (cutoff:3.500A) Processing helix chain '8' and resid 8 through 21 removed outlier: 3.554A pdb=" N THR 8 19 " --> pdb=" O SER 8 15 " (cutoff:3.500A) Processing helix chain '8' and resid 23 through 29 removed outlier: 3.568A pdb=" N SER 8 29 " --> pdb=" O GLN 8 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 15 Processing helix chain 'K' and resid 17 through 39 removed outlier: 3.811A pdb=" N SER K 21 " --> pdb=" O GLY K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 73 removed outlier: 3.934A pdb=" N LEU K 52 " --> pdb=" O SER K 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 15 removed outlier: 4.355A pdb=" N PHE L 8 " --> pdb=" O THR L 4 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 39 removed outlier: 4.139A pdb=" N SER L 21 " --> pdb=" O GLY L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 73 removed outlier: 3.892A pdb=" N LEU L 52 " --> pdb=" O SER L 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 15 removed outlier: 5.097A pdb=" N PHE M 8 " --> pdb=" O THR M 4 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE M 9 " --> pdb=" O ALA M 5 " (cutoff:3.500A) Processing helix chain 'M' and resid 18 through 39 removed outlier: 4.241A pdb=" N ILE M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN M 39 " --> pdb=" O GLY M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 73 removed outlier: 4.271A pdb=" N LEU M 52 " --> pdb=" O SER M 48 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N MET M 60 " --> pdb=" O LEU M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 15 Processing helix chain 'N' and resid 18 through 39 removed outlier: 3.638A pdb=" N GLY N 26 " --> pdb=" O GLY N 22 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ILE N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 74 removed outlier: 3.833A pdb=" N MET N 60 " --> pdb=" O LEU N 56 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 15 Processing helix chain 'O' and resid 17 through 39 removed outlier: 4.194A pdb=" N SER O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 74 removed outlier: 4.268A pdb=" N VAL O 67 " --> pdb=" O PHE O 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 15 Processing helix chain 'P' and resid 17 through 39 removed outlier: 4.115A pdb=" N SER P 21 " --> pdb=" O GLY P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 73 removed outlier: 3.737A pdb=" N CYS P 64 " --> pdb=" O MET P 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 15 Processing helix chain 'Q' and resid 17 through 39 removed outlier: 4.015A pdb=" N SER Q 21 " --> pdb=" O GLY Q 17 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 74 removed outlier: 4.619A pdb=" N MET Q 60 " --> pdb=" O LEU Q 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 16 removed outlier: 3.673A pdb=" N ILE R 9 " --> pdb=" O ALA R 5 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL R 16 " --> pdb=" O GLY R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 39 removed outlier: 4.091A pdb=" N SER R 21 " --> pdb=" O GLY R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 73 removed outlier: 3.762A pdb=" N MET R 60 " --> pdb=" O LEU R 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 10 Processing helix chain 'a' and resid 19 through 24 removed outlier: 3.852A pdb=" N ILE a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 31 Processing helix chain 'a' and resid 40 through 58 removed outlier: 4.072A pdb=" N GLN a 46 " --> pdb=" O PHE a 42 " (cutoff:3.500A) Processing helix chain 'a' and resid 62 through 67 Processing helix chain 'a' and resid 68 through 87 removed outlier: 3.634A pdb=" N LEU a 84 " --> pdb=" O GLY a 80 " (cutoff:3.500A) Processing helix chain 'a' and resid 93 through 96 Processing helix chain 'a' and resid 97 through 127 Proline residue: a 107 - end of helix removed outlier: 7.486A pdb=" N LYS a 122 " --> pdb=" O ARG a 118 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ALA a 123 " --> pdb=" O ASN a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 136 No H-bonds generated for 'chain 'a' and resid 134 through 136' Processing helix chain 'a' and resid 137 through 182 removed outlier: 4.665A pdb=" N ILE a 144 " --> pdb=" O MET a 140 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE a 147 " --> pdb=" O ILE a 143 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLN a 152 " --> pdb=" O SER a 148 " (cutoff:3.500A) Proline residue: a 153 - end of helix removed outlier: 3.656A pdb=" N LEU a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY a 167 " --> pdb=" O ASN a 163 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS a 172 " --> pdb=" O HIS a 168 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 225 removed outlier: 3.753A pdb=" N ALA a 189 " --> pdb=" O SER a 185 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET a 208 " --> pdb=" O PHE a 204 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 16 No H-bonds generated for 'chain 'b' and resid 14 through 16' Processing helix chain 'b' and resid 19 through 30 Proline residue: b 27 - end of helix Processing helix chain 'b' and resid 31 through 48 removed outlier: 4.626A pdb=" N TYR b 35 " --> pdb=" O VAL b 31 " (cutoff:3.500A) Processing helix chain 'b' and resid 54 through 112 removed outlier: 3.621A pdb=" N PHE b 58 " --> pdb=" O THR b 54 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ALA b 76 " --> pdb=" O LYS b 72 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N SER b 77 " --> pdb=" O LYS b 73 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL b 96 " --> pdb=" O GLN b 92 " (cutoff:3.500A) Processing helix chain 'd' and resid 114 through 122 removed outlier: 3.677A pdb=" N LYS d 120 " --> pdb=" O LYS d 116 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 130 Processing helix chain 'd' and resid 131 through 139 removed outlier: 3.877A pdb=" N GLU d 137 " --> pdb=" O GLU d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 143 removed outlier: 3.718A pdb=" N LYS d 143 " --> pdb=" O PRO d 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 140 through 143' Processing helix chain 'd' and resid 145 through 149 Processing helix chain 'e' and resid 7 through 57 Proline residue: e 34 - end of helix Processing helix chain 'f' and resid 18 through 26 Processing helix chain 'f' and resid 30 through 49 removed outlier: 3.856A pdb=" N ALA f 36 " --> pdb=" O GLY f 32 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG f 39 " --> pdb=" O GLY f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 56 through 74 removed outlier: 4.727A pdb=" N VAL f 62 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN f 70 " --> pdb=" O TYR f 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 75 through 80 removed outlier: 4.222A pdb=" N HIS f 80 " --> pdb=" O LYS f 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 37 removed outlier: 4.113A pdb=" N ARG g 25 " --> pdb=" O TYR g 21 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA g 27 " --> pdb=" O LYS g 23 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR g 32 " --> pdb=" O THR g 28 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N VAL g 35 " --> pdb=" O TYR g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 43 through 62 removed outlier: 4.551A pdb=" N THR g 47 " --> pdb=" O ALA g 43 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 67 Processing helix chain 'g' and resid 68 through 94 removed outlier: 3.568A pdb=" N TRP g 85 " --> pdb=" O GLU g 81 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N PHE g 86 " --> pdb=" O VAL g 82 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N TYR g 87 " --> pdb=" O TRP g 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 3 through 10 Processing helix chain 'j' and resid 13 through 19 Processing helix chain 'j' and resid 20 through 22 No H-bonds generated for 'chain 'j' and resid 20 through 22' Processing helix chain 'j' and resid 23 through 48 Processing helix chain 'k' and resid 13 through 18 Processing helix chain 'k' and resid 22 through 46 removed outlier: 3.879A pdb=" N ARG k 26 " --> pdb=" O THR k 22 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N MET k 27 " --> pdb=" O LEU k 23 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU k 46 " --> pdb=" O LEU k 42 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 12 through 13 825 hydrogen bonds defined for protein. 2427 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: 7.68 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10438 1.03 - 1.23: 265 1.23 - 1.43: 4165 1.43 - 1.62: 6307 1.62 - 1.82: 114 Bond restraints: 21289 Sorted by residual: bond pdb=" CA M3L N 43 " pdb=" HA M3L N 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.65e+01 bond pdb=" CA M3L O 43 " pdb=" HA M3L O 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" CA M3L M 43 " pdb=" HA M3L M 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.64e+01 bond pdb=" CA M3L P 43 " pdb=" HA M3L P 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" CA M3L Q 43 " pdb=" HA M3L Q 43 " ideal model delta sigma weight residual 0.970 1.133 -0.163 2.00e-02 2.50e+03 6.63e+01 ... (remaining 21284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 37871 2.48 - 4.97: 431 4.97 - 7.45: 69 7.45 - 9.93: 33 9.93 - 12.41: 8 Bond angle restraints: 38412 Sorted by residual: angle pdb=" C51 CDL b 302 " pdb=" CB5 CDL b 302 " pdb=" OB6 CDL b 302 " ideal model delta sigma weight residual 111.33 121.07 -9.74 1.32e+00 5.72e-01 5.43e+01 angle pdb=" C11 CDL b 302 " pdb=" CA5 CDL b 302 " pdb=" OA6 CDL b 302 " ideal model delta sigma weight residual 111.33 120.68 -9.35 1.32e+00 5.72e-01 5.00e+01 angle pdb=" C11 CDL a 301 " pdb=" CA5 CDL a 301 " pdb=" OA6 CDL a 301 " ideal model delta sigma weight residual 111.33 120.29 -8.96 1.32e+00 5.72e-01 4.59e+01 angle pdb=" C11 CDL b 301 " pdb=" CA5 CDL b 301 " pdb=" OA6 CDL b 301 " ideal model delta sigma weight residual 111.33 119.92 -8.59 1.32e+00 5.72e-01 4.22e+01 angle pdb=" C51 CDL a 301 " pdb=" CB5 CDL a 301 " pdb=" OB6 CDL a 301 " ideal model delta sigma weight residual 111.33 119.88 -8.55 1.32e+00 5.72e-01 4.18e+01 ... (remaining 38407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.26: 8916 20.26 - 40.52: 766 40.52 - 60.79: 408 60.79 - 81.05: 19 81.05 - 101.31: 8 Dihedral angle restraints: 10117 sinusoidal: 5579 harmonic: 4538 Sorted by residual: dihedral pdb=" CA LEU M 62 " pdb=" C LEU M 62 " pdb=" N PHE M 63 " pdb=" CA PHE M 63 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA LYS b 48 " pdb=" C LYS b 48 " pdb=" N GLU b 49 " pdb=" CA GLU b 49 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE M 29 " pdb=" C PHE M 29 " pdb=" N GLY M 30 " pdb=" CA GLY M 30 " ideal model delta harmonic sigma weight residual 180.00 159.42 20.58 0 5.00e+00 4.00e-02 1.69e+01 ... (remaining 10114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1068 0.034 - 0.069: 424 0.069 - 0.103: 111 0.103 - 0.137: 39 0.137 - 0.172: 9 Chirality restraints: 1651 Sorted by residual: chirality pdb=" CB ILE R 9 " pdb=" CA ILE R 9 " pdb=" CG1 ILE R 9 " pdb=" CG2 ILE R 9 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.38e-01 chirality pdb=" CA PRO a 89 " pdb=" N PRO a 89 " pdb=" C PRO a 89 " pdb=" CB PRO a 89 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.73e-01 chirality pdb=" CA LEU M 62 " pdb=" N LEU M 62 " pdb=" C LEU M 62 " pdb=" CB LEU M 62 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.43e-01 ... (remaining 1648 not shown) Planarity restraints: 2982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 101 " -0.067 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C8 LHG f 101 " 0.020 2.00e-02 2.50e+03 pdb=" O7 LHG f 101 " 0.021 2.00e-02 2.50e+03 pdb=" O9 LHG f 101 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG f 101 " -0.057 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C24 LHG f 101 " 0.017 2.00e-02 2.50e+03 pdb=" O10 LHG f 101 " 0.021 2.00e-02 2.50e+03 pdb=" O8 LHG f 101 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7 LHG f 102 " 0.054 2.00e-02 2.50e+03 3.14e-02 9.87e+00 pdb=" C8 LHG f 102 " -0.016 2.00e-02 2.50e+03 pdb=" O7 LHG f 102 " -0.017 2.00e-02 2.50e+03 pdb=" O9 LHG f 102 " -0.022 2.00e-02 2.50e+03 ... (remaining 2979 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 436 2.08 - 2.71: 36417 2.71 - 3.34: 64600 3.34 - 3.97: 76496 3.97 - 4.60: 122694 Nonbonded interactions: 300643 Sorted by model distance: nonbonded pdb="HH22 ARG a 36 " pdb=" O PRO b 3 " model vdw 1.453 2.450 nonbonded pdb=" O ILE R 2 " pdb=" H ALA R 6 " model vdw 1.491 2.450 nonbonded pdb=" OD1 ASN 8 32 " pdb=" H PHE 8 33 " model vdw 1.527 2.450 nonbonded pdb=" H THR d 131 " pdb=" OD2 ASP d 134 " model vdw 1.528 2.450 nonbonded pdb=" OE1 GLU d 113 " pdb=" H GLU d 113 " model vdw 1.532 2.450 ... (remaining 300638 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'K' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) selection = chain 'L' selection = (chain 'M' and resid 1 through 74) selection = (chain 'N' and resid 1 through 74) selection = (chain 'O' and resid 1 through 74) selection = (chain 'P' and (resid 1 through 42 or (resid 43 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name CM1 or \ name CM2 or name CM3 or name HA or name HB2 or name HB3 or name HG2 or name HG3 \ or name HD2 or name HD3 or name HE2 or name HE3 or name HM11 or name HM12 or na \ me HM13 or name HM21 or name HM22 or name HM23 or name HM31 or name HM32 or name \ HM33)) or resid 44 through 74)) selection = (chain 'Q' and resid 1 through 74) selection = (chain 'R' and resid 1 through 74) } 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: 9.150 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: 0.340 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 46.670 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.060 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.008 0.083 10697 Z= 0.483 Angle : 1.035 12.413 14408 Z= 0.515 Chirality : 0.042 0.172 1651 Planarity : 0.004 0.041 1726 Dihedral : 17.259 101.309 3971 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: -0.21 (0.24), residues: 1270 helix: 0.37 (0.16), residues: 1005 sheet: None (None), residues: 0 loop : -1.79 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP g 85 HIS 0.013 0.002 HIS b 8 PHE 0.036 0.002 PHE M 47 TYR 0.013 0.001 TYR N 49 ARG 0.014 0.001 ARG b 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.587 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: K 3 ASP cc_start: 0.8113 (m-30) cc_final: 0.7761 (m-30) REVERT: b 102 LYS cc_start: 0.9141 (tttt) cc_final: 0.8913 (tttt) REVERT: d 158 GLU cc_start: 0.8501 (pm20) cc_final: 0.8173 (pm20) REVERT: g 82 VAL cc_start: 0.9055 (m) cc_final: 0.8844 (p) outliers start: 0 outliers final: 0 residues processed: 250 average time/residue: 0.4310 time to fit residues: 160.0817 Evaluate side-chains 202 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10697 Z= 0.275 Angle : 0.660 6.812 14408 Z= 0.348 Chirality : 0.039 0.148 1651 Planarity : 0.005 0.062 1726 Dihedral : 14.385 107.901 1740 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.63 % Allowed : 8.92 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.12 (0.24), residues: 1270 helix: 0.49 (0.16), residues: 1037 sheet: None (None), residues: 0 loop : -1.38 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP 8 9 HIS 0.010 0.001 HIS b 8 PHE 0.027 0.002 PHE M 47 TYR 0.014 0.001 TYR f 71 ARG 0.007 0.001 ARG f 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 1.553 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: 8 10 LEU cc_start: 0.8911 (tp) cc_final: 0.8621 (tp) REVERT: K 3 ASP cc_start: 0.8052 (m-30) cc_final: 0.7675 (m-30) REVERT: K 54 PHE cc_start: 0.8213 (t80) cc_final: 0.7959 (t80) REVERT: P 63 PHE cc_start: 0.6513 (OUTLIER) cc_final: 0.6284 (p90) REVERT: b 49 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8648 (tm-30) REVERT: b 51 TYR cc_start: 0.8438 (t80) cc_final: 0.8180 (t80) REVERT: d 158 GLU cc_start: 0.8466 (pm20) cc_final: 0.8096 (pm20) REVERT: j 7 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7946 (mmmt) outliers start: 17 outliers final: 13 residues processed: 240 average time/residue: 0.4680 time to fit residues: 165.4862 Evaluate side-chains 217 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 203 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 84 MET Chi-restraints excluded: chain k residue 42 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 63 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10697 Z= 0.275 Angle : 0.624 6.223 14408 Z= 0.327 Chirality : 0.039 0.153 1651 Planarity : 0.004 0.060 1726 Dihedral : 13.354 108.413 1740 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.49 % Allowed : 11.31 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.47 (0.24), residues: 1270 helix: 0.71 (0.16), residues: 1039 sheet: None (None), residues: 0 loop : -1.13 (0.42), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 85 HIS 0.006 0.001 HIS b 8 PHE 0.018 0.001 PHE P 29 TYR 0.011 0.001 TYR f 71 ARG 0.005 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 224 time to evaluate : 1.810 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: K 3 ASP cc_start: 0.8083 (m-30) cc_final: 0.7689 (m-30) REVERT: P 63 PHE cc_start: 0.6537 (OUTLIER) cc_final: 0.6314 (p90) REVERT: d 158 GLU cc_start: 0.8508 (pm20) cc_final: 0.8129 (pm20) outliers start: 26 outliers final: 18 residues processed: 234 average time/residue: 0.4562 time to fit residues: 159.6678 Evaluate side-chains 218 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 33 ILE Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain j residue 35 VAL Chi-restraints excluded: chain k residue 42 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10697 Z= 0.229 Angle : 0.598 7.177 14408 Z= 0.312 Chirality : 0.038 0.178 1651 Planarity : 0.004 0.059 1726 Dihedral : 12.581 107.378 1740 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.11 % Allowed : 12.66 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 0.76 (0.24), residues: 1270 helix: 0.90 (0.16), residues: 1039 sheet: None (None), residues: 0 loop : -0.98 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP g 85 HIS 0.004 0.001 HIS b 8 PHE 0.020 0.001 PHE K 63 TYR 0.011 0.001 TYR f 71 ARG 0.004 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 229 time to evaluate : 1.520 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: K 3 ASP cc_start: 0.8054 (m-30) cc_final: 0.7670 (m-30) REVERT: K 54 PHE cc_start: 0.8232 (t80) cc_final: 0.8019 (t80) REVERT: P 63 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.6365 (p90) outliers start: 22 outliers final: 19 residues processed: 239 average time/residue: 0.4276 time to fit residues: 150.0411 Evaluate side-chains 229 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 209 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 9 ILE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 108 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10697 Z= 0.224 Angle : 0.582 7.516 14408 Z= 0.304 Chirality : 0.037 0.164 1651 Planarity : 0.004 0.032 1726 Dihedral : 11.826 106.959 1740 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.11 % Allowed : 13.14 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.24), residues: 1270 helix: 1.04 (0.16), residues: 1041 sheet: None (None), residues: 0 loop : -0.90 (0.43), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 85 HIS 0.004 0.001 HIS b 8 PHE 0.024 0.001 PHE K 63 TYR 0.010 0.001 TYR f 71 ARG 0.003 0.000 ARG b 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 220 time to evaluate : 1.586 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: K 3 ASP cc_start: 0.8022 (m-30) cc_final: 0.7628 (m-30) outliers start: 22 outliers final: 19 residues processed: 232 average time/residue: 0.4496 time to fit residues: 154.9221 Evaluate side-chains 231 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 212 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain M residue 63 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10697 Z= 0.252 Angle : 0.592 8.130 14408 Z= 0.309 Chirality : 0.038 0.157 1651 Planarity : 0.004 0.032 1726 Dihedral : 11.576 107.274 1740 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.11 % Allowed : 13.90 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.01 (0.24), residues: 1270 helix: 1.11 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -1.05 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.026 0.001 PHE K 63 TYR 0.010 0.001 TYR f 71 ARG 0.004 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 215 time to evaluate : 1.663 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: K 3 ASP cc_start: 0.8028 (m-30) cc_final: 0.7625 (m-30) REVERT: j 7 LYS cc_start: 0.8058 (mmmt) cc_final: 0.7709 (mmmt) outliers start: 22 outliers final: 21 residues processed: 228 average time/residue: 0.4521 time to fit residues: 153.3729 Evaluate side-chains 227 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 206 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10697 Z= 0.225 Angle : 0.580 8.121 14408 Z= 0.303 Chirality : 0.037 0.148 1651 Planarity : 0.004 0.032 1726 Dihedral : 11.273 106.588 1740 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.30 % Allowed : 14.29 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.24), residues: 1270 helix: 1.20 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -1.02 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.027 0.001 PHE K 63 TYR 0.010 0.001 TYR f 71 ARG 0.002 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 220 time to evaluate : 1.573 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: K 3 ASP cc_start: 0.8040 (m-30) cc_final: 0.7646 (m-30) REVERT: K 47 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7478 (m-80) REVERT: j 7 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7748 (mmmt) REVERT: j 23 GLU cc_start: 0.8324 (mp0) cc_final: 0.8116 (mp0) outliers start: 24 outliers final: 22 residues processed: 233 average time/residue: 0.4209 time to fit residues: 144.7506 Evaluate side-chains 231 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 71 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 109 optimal weight: 0.9990 chunk 115 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10697 Z= 0.232 Angle : 0.579 8.149 14408 Z= 0.303 Chirality : 0.038 0.157 1651 Planarity : 0.004 0.032 1726 Dihedral : 11.145 106.581 1740 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.59 % Allowed : 14.48 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.21 (0.24), residues: 1270 helix: 1.26 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -1.04 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.026 0.001 PHE K 63 TYR 0.010 0.001 TYR f 71 ARG 0.002 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 214 time to evaluate : 1.775 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: K 3 ASP cc_start: 0.8064 (m-30) cc_final: 0.7676 (m-30) REVERT: K 47 PHE cc_start: 0.7699 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: j 7 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7715 (mmmt) REVERT: j 23 GLU cc_start: 0.8330 (mp0) cc_final: 0.8125 (mp0) outliers start: 27 outliers final: 23 residues processed: 231 average time/residue: 0.4246 time to fit residues: 144.3199 Evaluate side-chains 233 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 209 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 61 ILE Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 101 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 73 optimal weight: 0.2980 chunk 118 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 45 GLN a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10697 Z= 0.204 Angle : 0.578 7.963 14408 Z= 0.300 Chirality : 0.037 0.161 1651 Planarity : 0.004 0.032 1726 Dihedral : 10.898 105.619 1740 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.88 % Allowed : 14.48 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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 (0.24), residues: 1270 helix: 1.34 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.028 0.001 PHE K 63 TYR 0.012 0.001 TYR Q 49 ARG 0.002 0.000 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 217 time to evaluate : 1.551 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: K 3 ASP cc_start: 0.8051 (m-30) cc_final: 0.7658 (m-30) REVERT: K 47 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: Q 47 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.6367 (t80) REVERT: j 7 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7680 (mmmt) outliers start: 30 outliers final: 24 residues processed: 235 average time/residue: 0.4326 time to fit residues: 148.9892 Evaluate side-chains 234 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain K residue 47 PHE Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 9 ILE Chi-restraints excluded: chain N residue 32 LEU Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain Q residue 47 PHE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 0.0970 chunk 105 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10697 Z= 0.241 Angle : 0.589 7.857 14408 Z= 0.309 Chirality : 0.038 0.159 1651 Planarity : 0.004 0.032 1726 Dihedral : 10.948 106.127 1740 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.59 % Allowed : 15.15 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.34 (0.24), residues: 1270 helix: 1.35 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -1.01 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.026 0.001 PHE K 63 TYR 0.011 0.001 TYR Q 49 ARG 0.003 0.000 ARG R 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 1.615 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: K 3 ASP cc_start: 0.8055 (m-30) cc_final: 0.7662 (m-30) REVERT: N 60 MET cc_start: 0.6934 (mmt) cc_final: 0.6676 (mmt) REVERT: Q 58 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7816 (mm-30) REVERT: R 60 MET cc_start: 0.7626 (tpp) cc_final: 0.7343 (tpt) REVERT: j 7 LYS cc_start: 0.7979 (mmmt) cc_final: 0.7676 (mmmt) outliers start: 27 outliers final: 24 residues processed: 229 average time/residue: 0.4440 time to fit residues: 150.5575 Evaluate side-chains 230 residues out of total 1043 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 206 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 32 LEU Chi-restraints excluded: chain L residue 41 SER Chi-restraints excluded: chain M residue 47 PHE Chi-restraints excluded: chain N residue 9 ILE Chi-restraints excluded: chain N residue 54 PHE Chi-restraints excluded: chain O residue 32 LEU Chi-restraints excluded: chain O residue 67 VAL Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain P residue 54 PHE Chi-restraints excluded: chain P residue 63 PHE Chi-restraints excluded: chain Q residue 33 ILE Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 64 CYS Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain b residue 43 LEU Chi-restraints excluded: chain b residue 56 GLU Chi-restraints excluded: chain b residue 57 THR Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 104 ILE Chi-restraints excluded: chain d residue 119 GLU Chi-restraints excluded: chain d residue 135 LEU Chi-restraints excluded: chain g residue 44 GLU Chi-restraints excluded: chain j residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 30 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 101 optimal weight: 0.0970 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 168 HIS ** d 129 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 = 0.3710 r_free = 0.3710 target = 0.107905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.088486 restraints weight = 72792.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.091686 restraints weight = 30157.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.093562 restraints weight = 18363.631| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10697 Z= 0.198 Angle : 0.582 8.033 14408 Z= 0.302 Chirality : 0.037 0.162 1651 Planarity : 0.004 0.035 1726 Dihedral : 10.699 104.853 1740 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.40 % Allowed : 15.44 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.13 % 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: 1.50 (0.24), residues: 1270 helix: 1.44 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : -0.87 (0.43), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP g 85 HIS 0.003 0.001 HIS b 8 PHE 0.027 0.001 PHE K 63 TYR 0.011 0.001 TYR Q 49 ARG 0.003 0.000 ARG e 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4724.98 seconds wall clock time: 83 minutes 30.56 seconds (5010.56 seconds total)