Starting phenix.real_space_refine on Thu May 15 13:59:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jqn_36576/05_2025/8jqn_36576.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jqn_36576/05_2025/8jqn_36576.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jqn_36576/05_2025/8jqn_36576.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jqn_36576/05_2025/8jqn_36576.map" model { file = "/net/cci-nas-00/data/ceres_data/8jqn_36576/05_2025/8jqn_36576.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jqn_36576/05_2025/8jqn_36576.cif" } resolution = 2.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5334 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 5610 2.51 5 N 1555 2.21 5 O 1700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8919 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 903 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 774 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "h" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 887 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "l" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 776 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 97} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "a" Number of atoms: 2794 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 352, 2788 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 352, 2788 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2860 Chain: "A" Number of atoms: 2785 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 354, 2778 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 354, 2778 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 334} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 2848 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER a 58 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER a 58 " occ=0.50 residue: pdb=" N AVAL A 60 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 60 " occ=0.50 Time building chain proxies: 8.46, per 1000 atoms: 0.95 Number of scatterers: 8919 At special positions: 0 Unit cell: (124.95, 79.05, 163.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1700 8.00 N 1555 7.00 C 5610 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 96 " distance=2.04 Simple disulfide: pdb=" SG CYS l 22 " - pdb=" SG CYS l 87 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 1.7 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2102 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 18 sheets defined 16.1% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.736A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.586A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 78 through 82 removed outlier: 3.611A pdb=" N ASP L 81 " --> pdb=" O GLN L 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU L 82 " --> pdb=" O VAL L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 82' Processing helix chain 'h' and resid 28 through 32 removed outlier: 3.692A pdb=" N TYR h 32 " --> pdb=" O PHE h 29 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 65 Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'h' and resid 101 through 105 removed outlier: 3.779A pdb=" N GLY h 105 " --> pdb=" O GLY h 102 " (cutoff:3.500A) Processing helix chain 'l' and resid 78 through 82 removed outlier: 3.573A pdb=" N ASP l 81 " --> pdb=" O GLN l 78 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 Processing helix chain 'a' and resid 61 through 82 removed outlier: 5.263A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 157 through 160 removed outlier: 4.478A pdb=" N PHE a 160 " --> pdb=" O ASP a 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 157 through 160' Processing helix chain 'a' and resid 180 through 183 removed outlier: 3.779A pdb=" N VAL a 183 " --> pdb=" O ASP a 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 180 through 183' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 removed outlier: 3.779A pdb=" N THR a 256 " --> pdb=" O HIS a 253 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 345 removed outlier: 3.577A pdb=" N ASN a 344 " --> pdb=" O PRO a 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 52 Processing helix chain 'A' and resid 61 through 82 removed outlier: 5.076A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.897A pdb=" N VAL A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.822A pdb=" N LEU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.615A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.512A pdb=" N TYR H 94 " --> pdb=" O THR H 112 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL H 37 " --> pdb=" O TYR H 95 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N MET H 34 " --> pdb=" O PHE H 50 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.772A pdb=" N ALA L 83 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.772A pdb=" N ALA L 83 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 17 through 23 removed outlier: 3.507A pdb=" N MET L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'h' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'h' and resid 11 through 12 removed outlier: 3.607A pdb=" N TYR h 94 " --> pdb=" O THR h 112 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET h 34 " --> pdb=" O PHE h 50 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N PHE h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'l' and resid 9 through 12 removed outlier: 6.652A pdb=" N TRP l 34 " --> pdb=" O VAL l 46 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'l' and resid 9 through 12 Processing sheet with id=AB1, first strand: chain 'l' and resid 18 through 23 removed outlier: 3.515A pdb=" N ALA l 18 " --> pdb=" O ILE l 74 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'a' and resid 2 through 7 removed outlier: 5.130A pdb=" N HIS A 1 " --> pdb=" O GLY A 18 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N HIS a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 87 through 90 removed outlier: 6.790A pdb=" N THR a 87 " --> pdb=" O PHE a 133 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL a 135 " --> pdb=" O THR a 87 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL a 89 " --> pdb=" O VAL a 135 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLY a 56 " --> pdb=" O ALA a 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 153 through 155 Processing sheet with id=AB5, first strand: chain 'a' and resid 329 through 331 removed outlier: 4.474A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 192 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N GLU A 205 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU A 212 " --> pdb=" O GLU A 205 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N LYS A 213 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N PHE A 277 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'a' and resid 284 through 287 removed outlier: 6.454A pdb=" N LYS a 284 " --> pdb=" O TRP a 311 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N CYS a 313 " --> pdb=" O LYS a 284 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N HIS a 286 " --> pdb=" O CYS a 313 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.515A pdb=" N ASP A 157 " --> pdb=" O TRP A 168 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.325A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 285 through 287 296 hydrogen bonds defined for protein. 729 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: 2.63 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1480 1.31 - 1.44: 2628 1.44 - 1.57: 4972 1.57 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 9156 Sorted by residual: bond pdb=" CA SER L 89 " pdb=" CB SER L 89 " ideal model delta sigma weight residual 1.534 1.436 0.098 1.34e-02 5.57e+03 5.40e+01 bond pdb=" C VAL a 167 " pdb=" O VAL a 167 " ideal model delta sigma weight residual 1.237 1.184 0.053 1.11e-02 8.12e+03 2.30e+01 bond pdb=" CA SER L 93 " pdb=" CB SER L 93 " ideal model delta sigma weight residual 1.530 1.458 0.072 1.68e-02 3.54e+03 1.84e+01 bond pdb=" N ARG A 336 " pdb=" CA ARG A 336 " ideal model delta sigma weight residual 1.453 1.488 -0.035 8.30e-03 1.45e+04 1.75e+01 bond pdb=" C SER L 89 " pdb=" O SER L 89 " ideal model delta sigma weight residual 1.235 1.193 0.042 1.08e-02 8.57e+03 1.52e+01 ... (remaining 9151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 12120 1.94 - 3.88: 295 3.88 - 5.83: 26 5.83 - 7.77: 7 7.77 - 9.71: 2 Bond angle restraints: 12450 Sorted by residual: angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 114.12 104.50 9.62 1.39e+00 5.18e-01 4.79e+01 angle pdb=" C LYS A 206 " pdb=" CA LYS A 206 " pdb=" CB LYS A 206 " ideal model delta sigma weight residual 110.16 100.45 9.71 1.66e+00 3.63e-01 3.42e+01 angle pdb=" C HIS a 158 " pdb=" CA HIS a 158 " pdb=" CB HIS a 158 " ideal model delta sigma weight residual 111.50 117.81 -6.31 1.29e+00 6.01e-01 2.39e+01 angle pdb=" N THR a 165 " pdb=" CA THR a 165 " pdb=" C THR a 165 " ideal model delta sigma weight residual 114.64 108.42 6.22 1.52e+00 4.33e-01 1.67e+01 angle pdb=" N ASN L 95 " pdb=" CA ASN L 95 " pdb=" C ASN L 95 " ideal model delta sigma weight residual 114.31 109.19 5.12 1.29e+00 6.01e-01 1.57e+01 ... (remaining 12445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5011 17.53 - 35.06: 324 35.06 - 52.59: 59 52.59 - 70.12: 14 70.12 - 87.66: 4 Dihedral angle restraints: 5412 sinusoidal: 2116 harmonic: 3296 Sorted by residual: dihedral pdb=" CB CYS a 291 " pdb=" SG CYS a 291 " pdb=" SG CYS a 312 " pdb=" CB CYS a 312 " ideal model delta sinusoidal sigma weight residual -86.00 -130.96 44.96 1 1.00e+01 1.00e-02 2.81e+01 dihedral pdb=" C HIS a 164 " pdb=" N HIS a 164 " pdb=" CA HIS a 164 " pdb=" CB HIS a 164 " ideal model delta harmonic sigma weight residual -122.60 -111.91 -10.69 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C LYS A 206 " pdb=" N LYS A 206 " pdb=" CA LYS A 206 " pdb=" CB LYS A 206 " ideal model delta harmonic sigma weight residual -122.60 -112.01 -10.59 0 2.50e+00 1.60e-01 1.79e+01 ... (remaining 5409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1055 0.055 - 0.110: 217 0.110 - 0.166: 51 0.166 - 0.221: 6 0.221 - 0.276: 1 Chirality restraints: 1330 Sorted by residual: chirality pdb=" CA HIS a 164 " pdb=" N HIS a 164 " pdb=" C HIS a 164 " pdb=" CB HIS a 164 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA LEU L 96 " pdb=" N LEU L 96 " pdb=" C LEU L 96 " pdb=" CB LEU L 96 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA GLN l 78 " pdb=" N GLN l 78 " pdb=" C GLN l 78 " pdb=" CB GLN l 78 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1327 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA l 77 " -0.022 2.00e-02 2.50e+03 4.50e-02 2.02e+01 pdb=" C ALA l 77 " 0.078 2.00e-02 2.50e+03 pdb=" O ALA l 77 " -0.030 2.00e-02 2.50e+03 pdb=" N GLN l 78 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE h 100 " 0.016 2.00e-02 2.50e+03 1.49e-02 3.90e+00 pdb=" CG PHE h 100 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE h 100 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE h 100 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE h 100 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE h 100 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE h 100 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR l 33 " -0.014 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR l 33 " 0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR l 33 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR l 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR l 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR l 33 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR l 33 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR l 33 " -0.000 2.00e-02 2.50e+03 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1509 2.76 - 3.30: 7748 3.30 - 3.83: 13916 3.83 - 4.37: 17037 4.37 - 4.90: 30629 Nonbonded interactions: 70839 Sorted by model distance: nonbonded pdb=" OG SER A 297 " pdb=" O TYR A 331 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP A 197 " pdb=" NZ LYS A 221 " model vdw 2.239 3.120 nonbonded pdb=" OE2 GLU L 82 " pdb=" N VAL L 107 " model vdw 2.241 3.120 nonbonded pdb=" OD2 ASP a 197 " pdb=" NZ LYS a 221 " model vdw 2.273 3.120 nonbonded pdb=" OG SER a 297 " pdb=" O TYR a 331 " model vdw 2.273 3.040 ... (remaining 70834 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 'A' and (resid 1 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB )) or resid 30 through 57 or resid 59 or resid 61 through \ 257 or (resid 258 and (name N or name CA or name C or name O or name CB )) or re \ sid 259 through 283 or (resid 284 and (name N or name CA or name C or name O or \ name CB )) or resid 285 through 309 or (resid 310 and (name N or name CA or name \ C or name O or name CB )) or resid 311 through 352)) selection = (chain 'a' and (resid 1 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 25 or (resid 26 through 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 or (resid 31 and (n \ ame N or name CA or name C or name O or name CB )) or resid 32 through 57 or res \ id 59 or resid 61 through 121 or (resid 122 and (name N or name CA or name C or \ name O or name CB )) or resid 123 through 124 or (resid 125 through 127 and (nam \ e N or name CA or name C or name O or name CB )) or resid 128 through 288 or (re \ sid 289 and (name N or name CA or name C or name O or name CB )) or resid 290 th \ rough 314 or (resid 315 and (name N or name CA or name C or name O or name CB )) \ or resid 316 through 325 or (resid 326 and (name N or name CA or name C or name \ O or name CB )) or resid 327 through 352)) } ncs_group { reference = (chain 'H' and (resid 2 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )) or resid 77 through 86 or (resid 87 through 88 and (nam \ e N or name CA or name C or name O or name CB )) or resid 89 through 117)) selection = chain 'h' } ncs_group { reference = (chain 'L' and (resid 4 through 79 or (resid 80 and (name N or name CA or name C \ or name O or name CB )) or resid 81 through 108)) selection = (chain 'l' and (resid 4 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 108)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.650 Find NCS groups from input model: 0.350 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 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 : 0.007 0.098 9172 Z= 0.362 Angle : 0.714 9.712 12482 Z= 0.448 Chirality : 0.049 0.276 1330 Planarity : 0.004 0.045 1606 Dihedral : 12.256 87.655 3262 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.80 % Favored : 94.11 % Rotamer: Outliers : 1.37 % Allowed : 0.84 % Favored : 97.79 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 7.14 % 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: -0.89 (0.25), residues: 1143 helix: 2.08 (0.59), residues: 73 sheet: -0.62 (0.28), residues: 369 loop : -0.84 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 168 HIS 0.009 0.001 HIS a 164 PHE 0.035 0.002 PHE h 100 TYR 0.031 0.002 TYR l 33 ARG 0.005 0.001 ARG a 261 Details of bonding type rmsd hydrogen bonds : bond 0.23039 ( 285) hydrogen bonds : angle 8.41074 ( 729) SS BOND : bond 0.00331 ( 16) SS BOND : angle 1.19182 ( 32) covalent geometry : bond 0.00683 ( 9156) covalent geometry : angle 0.71240 (12450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 11 VAL cc_start: 0.8306 (t) cc_final: 0.7992 (p) REVERT: H 43 LYS cc_start: 0.6206 (mppt) cc_final: 0.5854 (mtmt) REVERT: H 57 ASN cc_start: 0.8146 (m-40) cc_final: 0.7876 (m110) REVERT: H 71 SER cc_start: 0.8053 (t) cc_final: 0.7654 (p) REVERT: L 29 LYS cc_start: 0.6847 (mttt) cc_final: 0.6375 (mtmt) REVERT: L 62 SER cc_start: 0.7697 (t) cc_final: 0.7354 (m) REVERT: L 69 MET cc_start: 0.6794 (ttm) cc_final: 0.6536 (ttm) REVERT: L 84 ASP cc_start: 0.7431 (m-30) cc_final: 0.7102 (m-30) REVERT: h 78 THR cc_start: 0.6922 (m) cc_final: 0.6652 (t) REVERT: l 29 LYS cc_start: 0.5390 (mmmt) cc_final: 0.5105 (mttp) REVERT: l 60 ARG cc_start: 0.6761 (ptt180) cc_final: 0.6555 (ptt180) REVERT: l 82 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6286 (tp30) REVERT: a 10 LYS cc_start: 0.6736 (mttt) cc_final: 0.6329 (mttp) REVERT: a 11 LYS cc_start: 0.6850 (mtpt) cc_final: 0.5319 (tppt) REVERT: a 24 ASP cc_start: 0.7349 (p0) cc_final: 0.7061 (p0) REVERT: a 72 GLU cc_start: 0.6003 (tt0) cc_final: 0.5792 (tt0) REVERT: a 142 GLU cc_start: 0.6634 (tt0) cc_final: 0.6331 (mt-10) REVERT: a 156 GLU cc_start: 0.6427 (mt-10) cc_final: 0.6224 (mt-10) REVERT: a 165 THR cc_start: 0.5960 (OUTLIER) cc_final: 0.5461 (m) REVERT: a 166 SER cc_start: 0.7125 (OUTLIER) cc_final: 0.6869 (p) REVERT: a 170 LYS cc_start: 0.7620 (ptmm) cc_final: 0.7049 (ptmm) REVERT: a 189 LYS cc_start: 0.7770 (tptm) cc_final: 0.7014 (tptp) REVERT: a 192 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6832 (mm-30) REVERT: a 261 ARG cc_start: 0.7256 (mmm-85) cc_final: 0.6496 (mtp180) REVERT: a 264 MET cc_start: 0.7917 (mmt) cc_final: 0.7313 (mmt) REVERT: a 271 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7342 (mm-30) REVERT: a 279 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6897 (mt-10) REVERT: a 302 THR cc_start: 0.7665 (m) cc_final: 0.7051 (p) REVERT: A 10 LYS cc_start: 0.7677 (mptt) cc_final: 0.7313 (mmtt) REVERT: A 40 ARG cc_start: 0.6548 (mpp80) cc_final: 0.5863 (mtt90) REVERT: A 52 ASP cc_start: 0.6806 (t70) cc_final: 0.6556 (m-30) REVERT: A 109 ASN cc_start: 0.7143 (m-40) cc_final: 0.6847 (t0) REVERT: A 128 LYS cc_start: 0.6815 (tttp) cc_final: 0.6521 (ttmt) REVERT: A 130 ASN cc_start: 0.6839 (p0) cc_final: 0.6200 (m110) REVERT: A 138 ASP cc_start: 0.6764 (t0) cc_final: 0.6554 (m-30) REVERT: A 178 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6719 (mt-10) REVERT: A 209 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7464 (m) REVERT: A 274 GLU cc_start: 0.7685 (tt0) cc_final: 0.7387 (tt0) REVERT: A 284 LYS cc_start: 0.7909 (tttp) cc_final: 0.7073 (tptp) outliers start: 12 outliers final: 1 residues processed: 218 average time/residue: 1.2114 time to fit residues: 281.5177 Evaluate side-chains 155 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain l residue 82 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 165 THR Chi-restraints excluded: chain a residue 166 SER Chi-restraints excluded: chain A residue 209 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 0.0770 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 0.3980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN H 101 ASN L 41 GLN a 2 HIS a 82 ASN a 102 GLN a 131 ASN A 85 GLN A 131 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.141121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104185 restraints weight = 22649.608| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.93 r_work: 0.2892 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2906 r_free = 0.2906 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 9172 Z= 0.113 Angle : 0.577 7.484 12482 Z= 0.313 Chirality : 0.044 0.148 1330 Planarity : 0.004 0.040 1606 Dihedral : 5.101 40.829 1265 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.89 % Allowed : 8.61 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.68 (0.25), residues: 1143 helix: 1.82 (0.58), residues: 77 sheet: -0.52 (0.27), residues: 379 loop : -0.63 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 168 HIS 0.006 0.001 HIS a 2 PHE 0.021 0.002 PHE h 100 TYR 0.027 0.001 TYR H 103 ARG 0.009 0.001 ARG a 41 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 285) hydrogen bonds : angle 5.87630 ( 729) SS BOND : bond 0.00369 ( 16) SS BOND : angle 1.83063 ( 32) covalent geometry : bond 0.00247 ( 9156) covalent geometry : angle 0.57017 (12450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 1.077 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7048 (mppt) cc_final: 0.6784 (mtmt) REVERT: H 57 ASN cc_start: 0.8555 (m-40) cc_final: 0.8348 (m110) REVERT: H 71 SER cc_start: 0.8557 (t) cc_final: 0.8345 (p) REVERT: L 29 LYS cc_start: 0.7996 (mttt) cc_final: 0.7558 (mtpt) REVERT: L 62 SER cc_start: 0.8043 (t) cc_final: 0.7710 (p) REVERT: h 78 THR cc_start: 0.8023 (m) cc_final: 0.7813 (t) REVERT: l 29 LYS cc_start: 0.6801 (mmmt) cc_final: 0.6328 (mttp) REVERT: a 10 LYS cc_start: 0.7725 (mttt) cc_final: 0.7333 (mttp) REVERT: a 40 ARG cc_start: 0.7777 (mtm110) cc_final: 0.7443 (mtm-85) REVERT: a 110 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6537 (pt0) REVERT: a 136 ASP cc_start: 0.8232 (p0) cc_final: 0.7873 (p0) REVERT: a 139 THR cc_start: 0.8621 (p) cc_final: 0.8349 (p) REVERT: a 140 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7918 (mt) REVERT: a 156 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6612 (mt-10) REVERT: a 170 LYS cc_start: 0.8542 (ptmm) cc_final: 0.8202 (ptmm) REVERT: a 189 LYS cc_start: 0.8683 (tptm) cc_final: 0.8441 (tptp) REVERT: a 261 ARG cc_start: 0.8420 (mmm-85) cc_final: 0.8062 (mtp180) REVERT: a 264 MET cc_start: 0.9075 (mmt) cc_final: 0.8710 (mmt) REVERT: a 271 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7971 (mm-30) REVERT: A 10 LYS cc_start: 0.8262 (mptt) cc_final: 0.7953 (mmmt) REVERT: A 12 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7016 (mm-30) REVERT: A 40 ARG cc_start: 0.7634 (mpp80) cc_final: 0.7132 (mtt90) REVERT: A 50 TRP cc_start: 0.8452 (t-100) cc_final: 0.8143 (t-100) REVERT: A 109 ASN cc_start: 0.7478 (m-40) cc_final: 0.7242 (t0) REVERT: A 128 LYS cc_start: 0.7251 (tttp) cc_final: 0.6944 (ttmt) REVERT: A 130 ASN cc_start: 0.7228 (p0) cc_final: 0.6425 (m-40) REVERT: A 284 LYS cc_start: 0.8676 (tttp) cc_final: 0.8269 (tptp) outliers start: 17 outliers final: 8 residues processed: 164 average time/residue: 1.3176 time to fit residues: 229.5364 Evaluate side-chains 141 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 140 LEU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 53 optimal weight: 7.9990 chunk 87 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 41 GLN a 2 HIS ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.136566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099537 restraints weight = 26807.786| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.06 r_work: 0.2800 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 9172 Z= 0.252 Angle : 0.736 10.821 12482 Z= 0.393 Chirality : 0.051 0.262 1330 Planarity : 0.006 0.042 1606 Dihedral : 5.315 37.942 1259 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.84 % Allowed : 11.03 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.79 (0.25), residues: 1143 helix: 1.46 (0.56), residues: 77 sheet: -0.42 (0.27), residues: 374 loop : -0.79 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 168 HIS 0.008 0.002 HIS H 35 PHE 0.039 0.003 PHE h 100 TYR 0.029 0.002 TYR H 103 ARG 0.011 0.001 ARG a 257 Details of bonding type rmsd hydrogen bonds : bond 0.05503 ( 285) hydrogen bonds : angle 5.78760 ( 729) SS BOND : bond 0.00704 ( 16) SS BOND : angle 2.49336 ( 32) covalent geometry : bond 0.00607 ( 9156) covalent geometry : angle 0.72584 (12450) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7164 (mppt) cc_final: 0.6820 (mtpt) REVERT: H 57 ASN cc_start: 0.8627 (m-40) cc_final: 0.8396 (m110) REVERT: H 71 SER cc_start: 0.8535 (t) cc_final: 0.8327 (p) REVERT: L 23 SER cc_start: 0.8833 (p) cc_final: 0.8224 (t) REVERT: L 29 LYS cc_start: 0.8077 (mttt) cc_final: 0.7630 (mtmt) REVERT: L 62 SER cc_start: 0.8080 (t) cc_final: 0.7736 (p) REVERT: l 29 LYS cc_start: 0.7021 (mmmt) cc_final: 0.6554 (mttp) REVERT: a 10 LYS cc_start: 0.7688 (mttt) cc_final: 0.7391 (mttp) REVERT: a 40 ARG cc_start: 0.7799 (mtm110) cc_final: 0.7573 (mtt180) REVERT: a 74 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8060 (mt-10) REVERT: a 110 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6666 (pt0) REVERT: a 136 ASP cc_start: 0.8279 (p0) cc_final: 0.7913 (p0) REVERT: a 140 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8072 (mm) REVERT: a 170 LYS cc_start: 0.8542 (ptmm) cc_final: 0.8197 (ptmt) REVERT: a 189 LYS cc_start: 0.8765 (tptm) cc_final: 0.8530 (tptp) REVERT: a 261 ARG cc_start: 0.8528 (mmm-85) cc_final: 0.8126 (mtp180) REVERT: a 271 GLU cc_start: 0.8253 (mm-30) cc_final: 0.8048 (mm-30) REVERT: A 10 LYS cc_start: 0.8369 (mptt) cc_final: 0.8035 (mmmt) REVERT: A 12 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6985 (mm-30) REVERT: A 40 ARG cc_start: 0.7714 (mpp80) cc_final: 0.7140 (mtt90) REVERT: A 50 TRP cc_start: 0.8510 (t-100) cc_final: 0.8197 (t-100) REVERT: A 67 MET cc_start: 0.8528 (ttp) cc_final: 0.8304 (tmm) REVERT: A 109 ASN cc_start: 0.7517 (m-40) cc_final: 0.7226 (t0) REVERT: A 128 LYS cc_start: 0.7362 (tttp) cc_final: 0.7101 (tttt) REVERT: A 130 ASN cc_start: 0.7370 (p0) cc_final: 0.6493 (m110) REVERT: A 272 GLU cc_start: 0.8560 (tt0) cc_final: 0.8337 (tt0) REVERT: A 284 LYS cc_start: 0.8607 (tttp) cc_final: 0.8189 (tptp) REVERT: A 309 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7870 (pm20) outliers start: 26 outliers final: 14 residues processed: 144 average time/residue: 1.2927 time to fit residues: 197.8617 Evaluate side-chains 141 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 50 ASP Chi-restraints excluded: chain l residue 103 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 87 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 140 LEU Chi-restraints excluded: chain a residue 233 THR Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 309 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN L 41 GLN ** a 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.140102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.103008 restraints weight = 27489.144| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 3.16 r_work: 0.2851 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9172 Z= 0.116 Angle : 0.569 11.141 12482 Z= 0.306 Chirality : 0.044 0.204 1330 Planarity : 0.004 0.035 1606 Dihedral : 4.741 33.349 1259 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.21 % Allowed : 11.97 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.56 (0.25), residues: 1143 helix: 1.65 (0.57), residues: 77 sheet: -0.29 (0.27), residues: 374 loop : -0.62 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP a 168 HIS 0.005 0.001 HIS h 35 PHE 0.014 0.001 PHE h 100 TYR 0.023 0.001 TYR H 103 ARG 0.006 0.000 ARG a 41 Details of bonding type rmsd hydrogen bonds : bond 0.03886 ( 285) hydrogen bonds : angle 5.34754 ( 729) SS BOND : bond 0.00526 ( 16) SS BOND : angle 1.93458 ( 32) covalent geometry : bond 0.00271 ( 9156) covalent geometry : angle 0.56141 (12450) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7108 (mppt) cc_final: 0.6773 (mtpt) REVERT: H 57 ASN cc_start: 0.8637 (m-40) cc_final: 0.8400 (m110) REVERT: H 71 SER cc_start: 0.8527 (t) cc_final: 0.8313 (p) REVERT: L 29 LYS cc_start: 0.8010 (mttt) cc_final: 0.7540 (mtpt) REVERT: L 62 SER cc_start: 0.7975 (t) cc_final: 0.7625 (m) REVERT: l 29 LYS cc_start: 0.6885 (mmmt) cc_final: 0.6493 (mttp) REVERT: a 10 LYS cc_start: 0.7693 (mttt) cc_final: 0.7379 (mtmp) REVERT: a 170 LYS cc_start: 0.8439 (ptmm) cc_final: 0.8132 (ptmm) REVERT: a 189 LYS cc_start: 0.8665 (tptm) cc_final: 0.8433 (tptp) REVERT: a 261 ARG cc_start: 0.8453 (mmm-85) cc_final: 0.8009 (mtp180) REVERT: a 271 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8021 (mm-30) REVERT: A 10 LYS cc_start: 0.8318 (mptt) cc_final: 0.7974 (mtmp) REVERT: A 12 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7097 (mm-30) REVERT: A 40 ARG cc_start: 0.7592 (mpp80) cc_final: 0.7030 (mtt90) REVERT: A 109 ASN cc_start: 0.7469 (m-40) cc_final: 0.7221 (t0) REVERT: A 128 LYS cc_start: 0.7297 (tttp) cc_final: 0.6973 (ttmt) REVERT: A 130 ASN cc_start: 0.7382 (p0) cc_final: 0.6472 (m110) REVERT: A 284 LYS cc_start: 0.8600 (tttp) cc_final: 0.8190 (tptp) REVERT: A 309 GLU cc_start: 0.8094 (pm20) cc_final: 0.7869 (pm20) outliers start: 20 outliers final: 8 residues processed: 143 average time/residue: 1.2402 time to fit residues: 189.2008 Evaluate side-chains 133 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 125 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 63 MET Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 104 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 100 optimal weight: 0.0270 chunk 6 optimal weight: 6.9990 chunk 72 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 9 optimal weight: 0.0040 chunk 59 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN h 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.143360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.106414 restraints weight = 27696.033| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.31 r_work: 0.2892 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 9172 Z= 0.089 Angle : 0.525 12.152 12482 Z= 0.278 Chirality : 0.043 0.214 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.303 27.814 1259 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.21 % Allowed : 13.13 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.42 (0.26), residues: 1143 helix: 1.36 (0.57), residues: 77 sheet: -0.20 (0.27), residues: 381 loop : -0.46 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP a 168 HIS 0.005 0.001 HIS h 35 PHE 0.009 0.001 PHE a 277 TYR 0.022 0.001 TYR H 103 ARG 0.007 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03192 ( 285) hydrogen bonds : angle 5.08202 ( 729) SS BOND : bond 0.00383 ( 16) SS BOND : angle 1.62990 ( 32) covalent geometry : bond 0.00198 ( 9156) covalent geometry : angle 0.51902 (12450) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7040 (mppt) cc_final: 0.6673 (mtmt) REVERT: H 57 ASN cc_start: 0.8629 (m-40) cc_final: 0.8392 (m110) REVERT: H 71 SER cc_start: 0.8534 (t) cc_final: 0.8264 (p) REVERT: L 29 LYS cc_start: 0.7924 (mttt) cc_final: 0.7462 (mtpt) REVERT: L 62 SER cc_start: 0.7917 (t) cc_final: 0.7581 (m) REVERT: l 29 LYS cc_start: 0.6903 (mmmt) cc_final: 0.6375 (mttp) REVERT: l 69 MET cc_start: 0.8212 (tpp) cc_final: 0.7956 (mmt) REVERT: a 10 LYS cc_start: 0.7595 (mttt) cc_final: 0.7358 (mtmp) REVERT: a 72 GLU cc_start: 0.7436 (tt0) cc_final: 0.7235 (tt0) REVERT: a 170 LYS cc_start: 0.8496 (ptmm) cc_final: 0.8152 (ptmm) REVERT: a 189 LYS cc_start: 0.8575 (tptm) cc_final: 0.8343 (tptp) REVERT: a 261 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8036 (mtp180) REVERT: A 10 LYS cc_start: 0.8251 (mptt) cc_final: 0.7852 (mtmp) REVERT: A 12 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7120 (mm-30) REVERT: A 40 ARG cc_start: 0.7454 (mpp80) cc_final: 0.6995 (mtt90) REVERT: A 109 ASN cc_start: 0.7544 (m-40) cc_final: 0.7314 (t0) REVERT: A 128 LYS cc_start: 0.7262 (tttp) cc_final: 0.6936 (ttmt) REVERT: A 130 ASN cc_start: 0.7248 (p0) cc_final: 0.6446 (m110) REVERT: A 237 GLU cc_start: 0.7196 (pm20) cc_final: 0.6570 (mp0) REVERT: A 284 LYS cc_start: 0.8543 (tttp) cc_final: 0.8115 (tptp) REVERT: A 309 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7817 (pm20) outliers start: 20 outliers final: 10 residues processed: 155 average time/residue: 1.2655 time to fit residues: 209.0180 Evaluate side-chains 138 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 309 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 40 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 32 optimal weight: 4.9990 overall best weight: 1.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 2 HIS A 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101685 restraints weight = 28567.699| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 3.16 r_work: 0.2801 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9172 Z= 0.214 Angle : 0.676 13.956 12482 Z= 0.359 Chirality : 0.049 0.249 1330 Planarity : 0.005 0.041 1606 Dihedral : 5.075 38.373 1259 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.84 % Allowed : 13.34 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.49 (0.25), residues: 1143 helix: 1.40 (0.56), residues: 77 sheet: -0.11 (0.28), residues: 372 loop : -0.62 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP a 168 HIS 0.006 0.001 HIS H 35 PHE 0.026 0.002 PHE h 100 TYR 0.026 0.002 TYR H 103 ARG 0.007 0.001 ARG a 257 Details of bonding type rmsd hydrogen bonds : bond 0.04701 ( 285) hydrogen bonds : angle 5.39638 ( 729) SS BOND : bond 0.00706 ( 16) SS BOND : angle 2.37053 ( 32) covalent geometry : bond 0.00523 ( 9156) covalent geometry : angle 0.66615 (12450) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7269 (mppt) cc_final: 0.6901 (mtpt) REVERT: H 57 ASN cc_start: 0.8637 (m-40) cc_final: 0.8404 (m110) REVERT: H 71 SER cc_start: 0.8506 (t) cc_final: 0.8291 (p) REVERT: L 29 LYS cc_start: 0.8116 (mttt) cc_final: 0.7663 (mtmt) REVERT: L 49 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8607 (mt-10) REVERT: L 62 SER cc_start: 0.8030 (t) cc_final: 0.7712 (m) REVERT: h 18 LEU cc_start: 0.7438 (tp) cc_final: 0.6543 (mp) REVERT: h 104 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8375 (mt-10) REVERT: l 29 LYS cc_start: 0.7082 (mmmt) cc_final: 0.6602 (mttp) REVERT: l 69 MET cc_start: 0.8383 (tpp) cc_final: 0.8112 (mmt) REVERT: a 10 LYS cc_start: 0.7675 (mttt) cc_final: 0.7440 (mtmp) REVERT: a 40 ARG cc_start: 0.7880 (mtm180) cc_final: 0.7650 (mtt180) REVERT: a 74 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7983 (mt-10) REVERT: a 110 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6641 (pt0) REVERT: a 170 LYS cc_start: 0.8543 (ptmm) cc_final: 0.8197 (ptmm) REVERT: a 189 LYS cc_start: 0.8762 (tptm) cc_final: 0.8525 (tptp) REVERT: a 261 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8099 (mtp180) REVERT: A 10 LYS cc_start: 0.8274 (mptt) cc_final: 0.7892 (mtmp) REVERT: A 12 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7098 (mm-30) REVERT: A 40 ARG cc_start: 0.7660 (mpp80) cc_final: 0.7214 (mtt90) REVERT: A 109 ASN cc_start: 0.7561 (m-40) cc_final: 0.7328 (t0) REVERT: A 128 LYS cc_start: 0.7309 (tttp) cc_final: 0.7061 (tttt) REVERT: A 130 ASN cc_start: 0.7247 (p0) cc_final: 0.6442 (m110) REVERT: A 284 LYS cc_start: 0.8634 (tttp) cc_final: 0.8197 (tptp) outliers start: 26 outliers final: 14 residues processed: 143 average time/residue: 1.3157 time to fit residues: 199.8480 Evaluate side-chains 142 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 104 GLU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain l residue 5 THR Chi-restraints excluded: chain l residue 50 ASP Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 74 GLU Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 25 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 105 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.141527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102708 restraints weight = 19492.530| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.80 r_work: 0.2902 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 9172 Z= 0.103 Angle : 0.546 12.934 12482 Z= 0.291 Chirality : 0.043 0.206 1330 Planarity : 0.004 0.035 1606 Dihedral : 4.568 32.248 1259 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.68 % Allowed : 14.71 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.35 (0.26), residues: 1143 helix: 1.52 (0.57), residues: 77 sheet: -0.05 (0.28), residues: 372 loop : -0.50 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP a 168 HIS 0.003 0.001 HIS A 195 PHE 0.010 0.001 PHE a 277 TYR 0.022 0.001 TYR H 103 ARG 0.005 0.000 ARG a 41 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 285) hydrogen bonds : angle 5.11985 ( 729) SS BOND : bond 0.00498 ( 16) SS BOND : angle 1.76955 ( 32) covalent geometry : bond 0.00239 ( 9156) covalent geometry : angle 0.53979 (12450) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7170 (mppt) cc_final: 0.6768 (mtpt) REVERT: H 57 ASN cc_start: 0.8613 (m-40) cc_final: 0.8364 (m110) REVERT: H 71 SER cc_start: 0.8465 (t) cc_final: 0.8157 (p) REVERT: L 29 LYS cc_start: 0.7933 (mttt) cc_final: 0.7477 (mtpt) REVERT: L 62 SER cc_start: 0.7901 (t) cc_final: 0.7557 (m) REVERT: l 29 LYS cc_start: 0.6935 (mmmt) cc_final: 0.6467 (mttm) REVERT: l 69 MET cc_start: 0.8274 (tpp) cc_final: 0.7952 (mmt) REVERT: a 10 LYS cc_start: 0.7672 (mttt) cc_final: 0.7305 (mtmp) REVERT: a 40 ARG cc_start: 0.7818 (mtm180) cc_final: 0.7589 (mtt180) REVERT: a 51 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: a 110 GLU cc_start: 0.6976 (OUTLIER) cc_final: 0.6581 (pt0) REVERT: a 170 LYS cc_start: 0.8498 (ptmm) cc_final: 0.8098 (ptmm) REVERT: a 189 LYS cc_start: 0.8597 (tptm) cc_final: 0.8365 (tptp) REVERT: a 261 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.7939 (mtp180) REVERT: A 10 LYS cc_start: 0.8207 (mptt) cc_final: 0.7850 (mtmp) REVERT: A 12 GLU cc_start: 0.7581 (mt-10) cc_final: 0.7035 (mm-30) REVERT: A 40 ARG cc_start: 0.7420 (mpp80) cc_final: 0.6938 (mtt90) REVERT: A 109 ASN cc_start: 0.7550 (m-40) cc_final: 0.7336 (t0) REVERT: A 128 LYS cc_start: 0.7271 (tttp) cc_final: 0.6957 (ttmt) REVERT: A 130 ASN cc_start: 0.7216 (p0) cc_final: 0.6440 (m110) REVERT: A 237 GLU cc_start: 0.7144 (pm20) cc_final: 0.6677 (mp0) REVERT: A 284 LYS cc_start: 0.8499 (tttp) cc_final: 0.8065 (tptp) outliers start: 15 outliers final: 8 residues processed: 141 average time/residue: 1.3062 time to fit residues: 195.9630 Evaluate side-chains 134 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 85 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 105 optimal weight: 0.0870 chunk 84 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 106 optimal weight: 4.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.141046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103799 restraints weight = 23126.374| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.07 r_work: 0.2875 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9172 Z= 0.111 Angle : 0.554 12.470 12482 Z= 0.295 Chirality : 0.043 0.202 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.569 34.240 1259 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.68 % Allowed : 14.81 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.32 (0.26), residues: 1143 helix: 1.62 (0.58), residues: 77 sheet: -0.03 (0.28), residues: 371 loop : -0.48 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 168 HIS 0.004 0.001 HIS A 195 PHE 0.012 0.001 PHE a 277 TYR 0.024 0.001 TYR H 103 ARG 0.007 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03590 ( 285) hydrogen bonds : angle 5.08177 ( 729) SS BOND : bond 0.00504 ( 16) SS BOND : angle 1.82207 ( 32) covalent geometry : bond 0.00261 ( 9156) covalent geometry : angle 0.54698 (12450) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7173 (mppt) cc_final: 0.6770 (mtpt) REVERT: H 57 ASN cc_start: 0.8572 (m-40) cc_final: 0.8349 (m110) REVERT: H 71 SER cc_start: 0.8492 (t) cc_final: 0.8200 (p) REVERT: L 62 SER cc_start: 0.7944 (t) cc_final: 0.7621 (m) REVERT: l 29 LYS cc_start: 0.6966 (mmmt) cc_final: 0.6529 (mttp) REVERT: l 69 MET cc_start: 0.8228 (tpp) cc_final: 0.7890 (mmt) REVERT: a 10 LYS cc_start: 0.7716 (mttt) cc_final: 0.7485 (mtmp) REVERT: a 51 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6101 (mp0) REVERT: a 72 GLU cc_start: 0.7403 (tt0) cc_final: 0.7195 (tt0) REVERT: a 110 GLU cc_start: 0.6972 (OUTLIER) cc_final: 0.6583 (pt0) REVERT: a 140 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8179 (mt) REVERT: a 170 LYS cc_start: 0.8535 (ptmm) cc_final: 0.8153 (ptmm) REVERT: a 189 LYS cc_start: 0.8613 (tptm) cc_final: 0.8393 (tptp) REVERT: a 261 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.8011 (mtp180) REVERT: A 10 LYS cc_start: 0.8229 (mptt) cc_final: 0.7859 (mtmp) REVERT: A 12 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7060 (mm-30) REVERT: A 40 ARG cc_start: 0.7455 (mpp80) cc_final: 0.6958 (mtt90) REVERT: A 67 MET cc_start: 0.8232 (ttp) cc_final: 0.8029 (tmm) REVERT: A 109 ASN cc_start: 0.7600 (m-40) cc_final: 0.7391 (t0) REVERT: A 128 LYS cc_start: 0.7257 (tttp) cc_final: 0.6946 (ttmt) REVERT: A 130 ASN cc_start: 0.7215 (p0) cc_final: 0.6429 (m110) REVERT: A 237 GLU cc_start: 0.7177 (pm20) cc_final: 0.6771 (mp0) REVERT: A 284 LYS cc_start: 0.8567 (tttp) cc_final: 0.8147 (tptp) outliers start: 15 outliers final: 8 residues processed: 137 average time/residue: 1.2784 time to fit residues: 186.3448 Evaluate side-chains 136 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain a residue 51 GLU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 140 LEU Chi-restraints excluded: chain a residue 346 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 4 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 111 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 65 optimal weight: 0.0570 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.142043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.105182 restraints weight = 27386.129| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.17 r_work: 0.2870 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2883 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2883 r_free = 0.2883 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2883 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 9172 Z= 0.098 Angle : 0.533 13.330 12482 Z= 0.284 Chirality : 0.043 0.201 1330 Planarity : 0.004 0.034 1606 Dihedral : 4.438 32.309 1259 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.89 % Allowed : 14.92 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.24 (0.26), residues: 1143 helix: 1.70 (0.58), residues: 77 sheet: 0.01 (0.28), residues: 371 loop : -0.43 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP a 168 HIS 0.003 0.001 HIS A 195 PHE 0.011 0.001 PHE a 277 TYR 0.023 0.001 TYR H 103 ARG 0.007 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 285) hydrogen bonds : angle 5.01051 ( 729) SS BOND : bond 0.00460 ( 16) SS BOND : angle 1.66563 ( 32) covalent geometry : bond 0.00226 ( 9156) covalent geometry : angle 0.52733 (12450) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7177 (mppt) cc_final: 0.6761 (mtmt) REVERT: H 57 ASN cc_start: 0.8589 (m-40) cc_final: 0.8363 (m110) REVERT: H 71 SER cc_start: 0.8530 (t) cc_final: 0.8235 (p) REVERT: L 29 LYS cc_start: 0.7861 (mttm) cc_final: 0.7384 (mtpt) REVERT: L 62 SER cc_start: 0.7961 (t) cc_final: 0.7638 (m) REVERT: l 29 LYS cc_start: 0.6954 (mmmt) cc_final: 0.6551 (mttm) REVERT: l 69 MET cc_start: 0.8256 (tpp) cc_final: 0.7971 (mmt) REVERT: a 10 LYS cc_start: 0.7693 (mttt) cc_final: 0.7463 (mtmp) REVERT: a 72 GLU cc_start: 0.7431 (tt0) cc_final: 0.7222 (tt0) REVERT: a 110 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6573 (pt0) REVERT: a 140 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8215 (mt) REVERT: a 170 LYS cc_start: 0.8539 (ptmm) cc_final: 0.8131 (ptmm) REVERT: a 186 THR cc_start: 0.8913 (OUTLIER) cc_final: 0.8417 (m) REVERT: a 189 LYS cc_start: 0.8623 (tptm) cc_final: 0.8405 (tptp) REVERT: a 261 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.8050 (mtp180) REVERT: A 10 LYS cc_start: 0.8206 (mptt) cc_final: 0.7840 (mtmp) REVERT: A 12 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7109 (mm-30) REVERT: A 40 ARG cc_start: 0.7442 (mpp80) cc_final: 0.6959 (mtt90) REVERT: A 78 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7286 (mp) REVERT: A 128 LYS cc_start: 0.7309 (tttp) cc_final: 0.6995 (ttmt) REVERT: A 130 ASN cc_start: 0.7247 (p0) cc_final: 0.6387 (m110) REVERT: A 237 GLU cc_start: 0.7253 (pm20) cc_final: 0.6877 (mp0) REVERT: A 284 LYS cc_start: 0.8579 (tttp) cc_final: 0.8174 (tptp) outliers start: 17 outliers final: 11 residues processed: 139 average time/residue: 1.3607 time to fit residues: 201.8752 Evaluate side-chains 141 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 82 ASN Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 140 LEU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 97 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 111 optimal weight: 2.9990 chunk 22 optimal weight: 0.0370 chunk 8 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 overall best weight: 1.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.138452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.102444 restraints weight = 29488.101| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.24 r_work: 0.2799 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2766 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2766 r_free = 0.2766 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2766 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 9172 Z= 0.195 Angle : 0.659 14.080 12482 Z= 0.351 Chirality : 0.048 0.234 1330 Planarity : 0.005 0.039 1606 Dihedral : 5.027 37.837 1259 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.58 % Allowed : 15.34 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.40 (0.25), residues: 1143 helix: 1.48 (0.57), residues: 77 sheet: -0.01 (0.28), residues: 372 loop : -0.57 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP a 168 HIS 0.006 0.001 HIS H 35 PHE 0.021 0.002 PHE h 100 TYR 0.027 0.002 TYR H 103 ARG 0.007 0.001 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 285) hydrogen bonds : angle 5.30257 ( 729) SS BOND : bond 0.00668 ( 16) SS BOND : angle 2.32167 ( 32) covalent geometry : bond 0.00473 ( 9156) covalent geometry : angle 0.64942 (12450) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 43 LYS cc_start: 0.7300 (mppt) cc_final: 0.6888 (mtpt) REVERT: H 57 ASN cc_start: 0.8644 (m-40) cc_final: 0.8420 (m110) REVERT: H 71 SER cc_start: 0.8534 (t) cc_final: 0.8318 (p) REVERT: L 49 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8581 (mt-10) REVERT: L 62 SER cc_start: 0.8075 (t) cc_final: 0.7746 (m) REVERT: h 43 LYS cc_start: 0.7662 (mmtp) cc_final: 0.7395 (mmpt) REVERT: l 29 LYS cc_start: 0.7104 (mmmt) cc_final: 0.6647 (mttm) REVERT: l 69 MET cc_start: 0.8331 (tpp) cc_final: 0.8025 (mmt) REVERT: a 10 LYS cc_start: 0.7785 (mttt) cc_final: 0.7524 (mtmp) REVERT: a 170 LYS cc_start: 0.8620 (ptmm) cc_final: 0.8215 (ptmm) REVERT: a 189 LYS cc_start: 0.8764 (tptm) cc_final: 0.8526 (tptp) REVERT: a 261 ARG cc_start: 0.8543 (mmm-85) cc_final: 0.8094 (mtp180) REVERT: A 10 LYS cc_start: 0.8273 (mptt) cc_final: 0.7899 (mtmp) REVERT: A 12 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7103 (mm-30) REVERT: A 40 ARG cc_start: 0.7644 (mpp80) cc_final: 0.7178 (mtt90) REVERT: A 78 ILE cc_start: 0.7570 (OUTLIER) cc_final: 0.7307 (mp) REVERT: A 128 LYS cc_start: 0.7304 (tttp) cc_final: 0.7053 (tttt) REVERT: A 130 ASN cc_start: 0.7216 (p0) cc_final: 0.6430 (m110) REVERT: A 237 GLU cc_start: 0.7274 (pm20) cc_final: 0.6847 (mp0) REVERT: A 239 SER cc_start: 0.8941 (m) cc_final: 0.8730 (p) REVERT: A 284 LYS cc_start: 0.8637 (tttp) cc_final: 0.8199 (tptp) outliers start: 14 outliers final: 11 residues processed: 136 average time/residue: 1.2141 time to fit residues: 176.1438 Evaluate side-chains 139 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 90 THR Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain a residue 57 ILE Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 110 GLU Chi-restraints excluded: chain a residue 186 THR Chi-restraints excluded: chain a residue 346 VAL Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 97 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 106 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.102205 restraints weight = 18243.809| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.66 r_work: 0.2903 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9172 Z= 0.120 Angle : 0.570 13.547 12482 Z= 0.305 Chirality : 0.044 0.209 1330 Planarity : 0.004 0.033 1606 Dihedral : 4.738 34.296 1259 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.47 % Allowed : 15.44 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -0.36 (0.25), residues: 1143 helix: 1.56 (0.57), residues: 77 sheet: -0.02 (0.28), residues: 372 loop : -0.53 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP a 168 HIS 0.004 0.001 HIS A 195 PHE 0.012 0.001 PHE a 277 TYR 0.024 0.001 TYR H 103 ARG 0.007 0.000 ARG L 53 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 285) hydrogen bonds : angle 5.16826 ( 729) SS BOND : bond 0.00538 ( 16) SS BOND : angle 1.89145 ( 32) covalent geometry : bond 0.00284 ( 9156) covalent geometry : angle 0.56297 (12450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7564.26 seconds wall clock time: 130 minutes 49.17 seconds (7849.17 seconds total)