Starting phenix.real_space_refine on Fri Dec 27 18:36:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw4_41658/12_2024/8tw4_41658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw4_41658/12_2024/8tw4_41658.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tw4_41658/12_2024/8tw4_41658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw4_41658/12_2024/8tw4_41658.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw4_41658/12_2024/8tw4_41658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw4_41658/12_2024/8tw4_41658.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4076 2.51 5 N 1041 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6401 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1394 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain breaks: 8 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1815 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 228} Chain breaks: 5 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 625 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 710 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "X" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 129 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 116 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.70, per 1000 atoms: 0.73 Number of scatterers: 6401 At special positions: 0 Unit cell: (95.04, 87.48, 110.16, 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 41 16.00 O 1243 8.00 N 1041 7.00 C 4076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 110 " distance=2.04 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 228 " distance=2.04 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.02 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS Y 32 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 302 " - " ASN A 41 " " NAG C 1 " - " ASN A 82 " " NAG G 201 " - " ASN G 92 " " NAG H 1 " - " ASN D 74 " " NAG I 1 " - " ASN G 52 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1554 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 16 sheets defined 20.2% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.968A pdb=" N ASN A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.543A pdb=" N MET A 188 " --> pdb=" O MET A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.851A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.528A pdb=" N PHE A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.833A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 157 removed outlier: 3.573A pdb=" N ILE B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.750A pdb=" N LEU B 285 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.579A pdb=" N MET B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 129 through 135 Processing helix chain 'E' and resid 135 through 144 Processing helix chain 'D' and resid 101 through 114 removed outlier: 4.001A pdb=" N GLY D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 128 through 129 No H-bonds generated for 'chain 'G' and resid 128 through 129' Processing helix chain 'X' and resid 32 through 36 Processing helix chain 'X' and resid 37 through 39 No H-bonds generated for 'chain 'X' and resid 37 through 39' Processing helix chain 'X' and resid 40 through 48 removed outlier: 3.606A pdb=" N ILE X 45 " --> pdb=" O ILE X 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 46 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.436A pdb=" N VAL A 32 " --> pdb=" O ILE A 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.682A pdb=" N LEU A 40 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 94 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68 removed outlier: 3.648A pdb=" N LEU A 67 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 108 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 144 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 65 removed outlier: 3.761A pdb=" N TRP B 53 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 142 through 145 removed outlier: 4.668A pdb=" N GLU B 142 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 182 through 183 removed outlier: 3.532A pdb=" N VAL B 230 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 37 through 41 removed outlier: 4.052A pdb=" N LYS E 37 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 39 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 83 " --> pdb=" O GLY E 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.915A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 94 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.573A pdb=" N LYS F 37 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 57 through 59 Processing sheet with id=AB4, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.673A pdb=" N TYR F 113 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE G 53 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE G 64 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TRP G 55 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.602A pdb=" N GLY G 75 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU G 44 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN G 73 " --> pdb=" O LEU G 44 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 462 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: 1.57 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1992 1.34 - 1.46: 1459 1.46 - 1.58: 3017 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6522 Sorted by residual: bond pdb=" N VAL E 118 " pdb=" CA VAL E 118 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N CYS E 122 " pdb=" CA CYS E 122 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.17e-02 7.31e+03 8.55e+00 bond pdb=" N GLU E 120 " pdb=" CA GLU E 120 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.00e-02 1.00e+04 8.06e+00 bond pdb=" N CYS E 119 " pdb=" CA CYS E 119 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.61e+00 bond pdb=" N ASN E 121 " pdb=" CA ASN E 121 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.10e+00 ... (remaining 6517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 8786 3.50 - 7.01: 80 7.01 - 10.51: 4 10.51 - 14.02: 0 14.02 - 17.52: 1 Bond angle restraints: 8871 Sorted by residual: angle pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " pdb=" C5 NAG I 1 " ideal model delta sigma weight residual 113.21 130.73 -17.52 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C MET D 92 " pdb=" CA MET D 92 " pdb=" CB MET D 92 " ideal model delta sigma weight residual 116.54 110.14 6.40 1.15e+00 7.56e-01 3.10e+01 angle pdb=" C LYS G 51 " pdb=" N ASN G 52 " pdb=" CA ASN G 52 " ideal model delta sigma weight residual 121.89 130.81 -8.92 1.74e+00 3.30e-01 2.63e+01 angle pdb=" N CYS Y 32 " pdb=" CA CYS Y 32 " pdb=" C CYS Y 32 " ideal model delta sigma weight residual 114.31 109.06 5.25 1.29e+00 6.01e-01 1.66e+01 angle pdb=" C LEU D 29 " pdb=" N GLU D 30 " pdb=" CA GLU D 30 " ideal model delta sigma weight residual 121.54 128.52 -6.98 1.91e+00 2.74e-01 1.34e+01 ... (remaining 8866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 3542 16.87 - 33.74: 395 33.74 - 50.61: 118 50.61 - 67.48: 33 67.48 - 84.35: 12 Dihedral angle restraints: 4100 sinusoidal: 1706 harmonic: 2394 Sorted by residual: dihedral pdb=" CB CYS D 37 " pdb=" SG CYS D 37 " pdb=" SG CYS D 73 " pdb=" CB CYS D 73 " ideal model delta sinusoidal sigma weight residual -86.00 -161.22 75.22 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 122 " pdb=" CB CYS E 122 " ideal model delta sinusoidal sigma weight residual -86.00 -152.98 66.98 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 109 " pdb=" CB CYS A 109 " ideal model delta sinusoidal sigma weight residual 93.00 147.01 -54.01 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 4097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 989 0.090 - 0.181: 62 0.181 - 0.271: 3 0.271 - 0.362: 1 0.362 - 0.452: 1 Chirality restraints: 1056 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.72e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.74e+00 ... (remaining 1053 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 52 " 0.067 2.00e-02 2.50e+03 6.67e-02 5.55e+01 pdb=" CG ASN G 52 " -0.099 2.00e-02 2.50e+03 pdb=" OD1 ASN G 52 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN G 52 " -0.058 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 52 " 0.023 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" CG ASN G 52 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN G 52 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN G 52 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 74 " 0.029 2.00e-02 2.50e+03 2.74e-02 9.38e+00 pdb=" CG ASN D 74 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN D 74 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 74 " -0.029 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.029 2.00e-02 2.50e+03 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 160 2.66 - 3.22: 6236 3.22 - 3.78: 9795 3.78 - 4.34: 12830 4.34 - 4.90: 20352 Nonbonded interactions: 49373 Sorted by model distance: nonbonded pdb=" O ASP A 174 " pdb=" OG SER A 199 " model vdw 2.104 3.040 nonbonded pdb=" NH1 ARG E 117 " pdb=" O CYS D 96 " model vdw 2.132 3.120 nonbonded pdb=" OG SER B 254 " pdb=" OE2 GLU B 256 " model vdw 2.150 3.040 nonbonded pdb=" NE2 GLN B 25 " pdb=" O GLU B 125 " model vdw 2.203 3.120 nonbonded pdb=" O GLU A 36 " pdb=" OG SER A 99 " model vdw 2.228 3.040 ... (remaining 49368 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 'C' selection = chain 'H' } ncs_group { reference = (chain 'X' and (resid 32 or (resid 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 43 or (resid 44 and (name N or n \ ame CA or name C or name O or name CB )) or resid 45 through 46)) selection = (chain 'Y' and (resid 32 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 46)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.290 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6522 Z= 0.239 Angle : 0.862 17.520 8871 Z= 0.453 Chirality : 0.049 0.452 1056 Planarity : 0.005 0.088 1106 Dihedral : 16.307 84.354 2507 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.33 % Favored : 92.42 % Rotamer: Outliers : 3.91 % Allowed : 22.81 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.23 (0.27), residues: 778 helix: -1.96 (0.42), residues: 115 sheet: -0.40 (0.37), residues: 184 loop : -1.87 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 59 HIS 0.003 0.001 HIS E 61 PHE 0.030 0.002 PHE G 118 TYR 0.019 0.002 TYR B 291 ARG 0.010 0.001 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.6399 (ptpt) cc_final: 0.5903 (mmtm) REVERT: A 149 LYS cc_start: 0.9035 (tmtt) cc_final: 0.8637 (mmtt) REVERT: B 38 MET cc_start: 0.6639 (tpp) cc_final: 0.6116 (tpp) REVERT: B 168 PHE cc_start: 0.4745 (OUTLIER) cc_final: 0.3340 (p90) REVERT: B 252 ILE cc_start: 0.4803 (OUTLIER) cc_final: 0.4570 (tp) REVERT: E 89 GLU cc_start: 0.7600 (pt0) cc_final: 0.7307 (pt0) REVERT: E 125 MET cc_start: 0.5703 (pmm) cc_final: 0.5484 (pmm) REVERT: D 92 MET cc_start: 0.4834 (mmm) cc_final: 0.4476 (mmm) REVERT: G 108 ILE cc_start: 0.2528 (OUTLIER) cc_final: 0.1981 (pt) outliers start: 25 outliers final: 18 residues processed: 106 average time/residue: 0.1970 time to fit residues: 27.3894 Evaluate side-chains 100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain Y residue 40 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN E 61 HIS G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5869 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6522 Z= 0.229 Angle : 0.789 11.768 8871 Z= 0.394 Chirality : 0.047 0.415 1056 Planarity : 0.005 0.053 1106 Dihedral : 10.052 56.928 1237 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 5.94 % Allowed : 20.16 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.14 (0.28), residues: 778 helix: -1.57 (0.42), residues: 119 sheet: -0.20 (0.37), residues: 183 loop : -1.97 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 PHE 0.029 0.002 PHE G 118 TYR 0.022 0.002 TYR B 291 ARG 0.005 0.001 ARG E 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.9054 (tmtt) cc_final: 0.8621 (mmtt) REVERT: B 38 MET cc_start: 0.6590 (tpp) cc_final: 0.5867 (tpp) REVERT: B 155 HIS cc_start: 0.6118 (OUTLIER) cc_final: 0.5889 (p-80) REVERT: B 168 PHE cc_start: 0.4615 (OUTLIER) cc_final: 0.3248 (p90) REVERT: E 89 GLU cc_start: 0.8105 (pt0) cc_final: 0.7848 (pt0) REVERT: F 111 TYR cc_start: 0.5589 (OUTLIER) cc_final: 0.4376 (t80) REVERT: D 92 MET cc_start: 0.4486 (mmm) cc_final: 0.4117 (mmm) REVERT: D 94 GLN cc_start: 0.4775 (OUTLIER) cc_final: 0.4058 (pm20) outliers start: 38 outliers final: 19 residues processed: 107 average time/residue: 0.1769 time to fit residues: 26.0189 Evaluate side-chains 100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.0570 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6522 Z= 0.265 Angle : 0.776 9.612 8871 Z= 0.394 Chirality : 0.047 0.419 1056 Planarity : 0.005 0.055 1106 Dihedral : 9.454 58.300 1218 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.46 % Favored : 92.42 % Rotamer: Outliers : 5.62 % Allowed : 21.41 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.21 (0.28), residues: 778 helix: -1.63 (0.44), residues: 116 sheet: -0.28 (0.37), residues: 182 loop : -2.00 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 PHE 0.042 0.002 PHE Y 40 TYR 0.024 0.002 TYR B 291 ARG 0.006 0.001 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 77 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8704 (tp30) cc_final: 0.8211 (tp30) REVERT: A 87 LYS cc_start: 0.6542 (ptpt) cc_final: 0.5932 (tptt) REVERT: B 38 MET cc_start: 0.6785 (tpp) cc_final: 0.6145 (tpp) REVERT: B 155 HIS cc_start: 0.6162 (OUTLIER) cc_final: 0.5953 (p-80) REVERT: B 168 PHE cc_start: 0.4798 (OUTLIER) cc_final: 0.3307 (p90) REVERT: E 72 ASP cc_start: 0.8545 (t0) cc_final: 0.8305 (t0) REVERT: E 89 GLU cc_start: 0.8014 (pt0) cc_final: 0.7797 (pt0) REVERT: E 99 TYR cc_start: 0.3606 (OUTLIER) cc_final: 0.2844 (t80) REVERT: F 111 TYR cc_start: 0.5727 (OUTLIER) cc_final: 0.4637 (t80) REVERT: D 30 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6729 (pm20) REVERT: D 80 LYS cc_start: 0.7688 (tptp) cc_final: 0.7482 (tptt) REVERT: D 92 MET cc_start: 0.5042 (mmm) cc_final: 0.4581 (mmm) REVERT: D 94 GLN cc_start: 0.4680 (OUTLIER) cc_final: 0.4366 (pt0) outliers start: 36 outliers final: 21 residues processed: 106 average time/residue: 0.1861 time to fit residues: 26.3507 Evaluate side-chains 99 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 76 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5919 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6522 Z= 0.202 Angle : 0.735 9.879 8871 Z= 0.369 Chirality : 0.046 0.417 1056 Planarity : 0.004 0.049 1106 Dihedral : 9.199 56.190 1216 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 4.69 % Allowed : 23.28 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.16 (0.28), residues: 778 helix: -1.53 (0.43), residues: 116 sheet: -0.38 (0.38), residues: 175 loop : -1.89 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 PHE 0.039 0.002 PHE Y 40 TYR 0.021 0.001 TYR B 291 ARG 0.005 0.001 ARG E 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8716 (tp30) cc_final: 0.8264 (tp30) REVERT: A 149 LYS cc_start: 0.9019 (tmtt) cc_final: 0.8556 (mmtt) REVERT: B 168 PHE cc_start: 0.4511 (OUTLIER) cc_final: 0.3130 (p90) REVERT: E 72 ASP cc_start: 0.8198 (t0) cc_final: 0.7863 (t0) REVERT: E 89 GLU cc_start: 0.8018 (pt0) cc_final: 0.7753 (pt0) REVERT: E 99 TYR cc_start: 0.4025 (OUTLIER) cc_final: 0.3069 (t80) REVERT: F 111 TYR cc_start: 0.5665 (OUTLIER) cc_final: 0.4586 (t80) REVERT: D 30 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6817 (pt0) REVERT: D 92 MET cc_start: 0.5254 (mmm) cc_final: 0.4757 (mmm) outliers start: 30 outliers final: 22 residues processed: 104 average time/residue: 0.1675 time to fit residues: 23.8566 Evaluate side-chains 98 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 104 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 6522 Z= 0.296 Angle : 0.795 9.992 8871 Z= 0.405 Chirality : 0.047 0.432 1056 Planarity : 0.005 0.056 1106 Dihedral : 9.497 58.436 1216 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 21.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.48 % Favored : 91.39 % Rotamer: Outliers : 6.09 % Allowed : 22.97 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.42 (0.28), residues: 778 helix: -1.92 (0.41), residues: 117 sheet: -0.68 (0.37), residues: 179 loop : -1.97 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 55 HIS 0.005 0.001 HIS B 155 PHE 0.039 0.003 PHE A 263 TYR 0.025 0.002 TYR B 291 ARG 0.005 0.001 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 75 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8745 (tp30) cc_final: 0.8509 (tp30) REVERT: B 168 PHE cc_start: 0.4832 (OUTLIER) cc_final: 0.3300 (p90) REVERT: E 72 ASP cc_start: 0.8329 (t0) cc_final: 0.8042 (t0) REVERT: E 89 GLU cc_start: 0.7759 (pt0) cc_final: 0.7411 (pt0) REVERT: E 99 TYR cc_start: 0.4015 (OUTLIER) cc_final: 0.2832 (t80) REVERT: F 111 TYR cc_start: 0.5949 (OUTLIER) cc_final: 0.4950 (t80) REVERT: D 30 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7046 (pm20) REVERT: D 43 TRP cc_start: 0.8957 (OUTLIER) cc_final: 0.8285 (p90) REVERT: D 92 MET cc_start: 0.5563 (mmm) cc_final: 0.4758 (mmt) REVERT: G 108 ILE cc_start: 0.3223 (OUTLIER) cc_final: 0.2635 (pt) outliers start: 39 outliers final: 27 residues processed: 108 average time/residue: 0.1662 time to fit residues: 24.5668 Evaluate side-chains 103 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 70 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 62 optimal weight: 8.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5965 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6522 Z= 0.186 Angle : 0.747 10.103 8871 Z= 0.371 Chirality : 0.046 0.421 1056 Planarity : 0.004 0.048 1106 Dihedral : 9.173 59.199 1214 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.44 % Rotamer: Outliers : 4.69 % Allowed : 25.62 % Favored : 69.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.24 (0.29), residues: 778 helix: -1.60 (0.45), residues: 117 sheet: -0.66 (0.37), residues: 177 loop : -1.85 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 53 HIS 0.003 0.001 HIS B 155 PHE 0.042 0.002 PHE A 263 TYR 0.018 0.001 TYR B 291 ARG 0.005 0.001 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 75 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8680 (tp30) cc_final: 0.8100 (tp30) REVERT: A 149 LYS cc_start: 0.8980 (tmtt) cc_final: 0.8545 (mmtt) REVERT: A 157 LEU cc_start: 0.4699 (pp) cc_final: 0.4427 (pp) REVERT: A 188 MET cc_start: 0.8486 (ptt) cc_final: 0.7640 (tmm) REVERT: B 168 PHE cc_start: 0.4656 (OUTLIER) cc_final: 0.3320 (p90) REVERT: E 72 ASP cc_start: 0.8320 (t0) cc_final: 0.8020 (t0) REVERT: E 89 GLU cc_start: 0.8177 (pt0) cc_final: 0.7859 (pt0) REVERT: E 99 TYR cc_start: 0.3708 (OUTLIER) cc_final: 0.2724 (t80) REVERT: F 111 TYR cc_start: 0.5790 (OUTLIER) cc_final: 0.4817 (t80) REVERT: D 94 GLN cc_start: 0.4819 (OUTLIER) cc_final: 0.4517 (pt0) REVERT: G 108 ILE cc_start: 0.3077 (OUTLIER) cc_final: 0.2555 (pt) outliers start: 30 outliers final: 21 residues processed: 102 average time/residue: 0.1456 time to fit residues: 21.1953 Evaluate side-chains 98 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6522 Z= 0.255 Angle : 0.769 9.398 8871 Z= 0.386 Chirality : 0.047 0.430 1056 Planarity : 0.005 0.054 1106 Dihedral : 9.130 58.577 1212 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.87 % Favored : 91.00 % Rotamer: Outliers : 5.31 % Allowed : 26.09 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.29 (0.28), residues: 778 helix: -1.66 (0.43), residues: 117 sheet: -0.88 (0.36), residues: 175 loop : -1.79 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 59 HIS 0.004 0.001 HIS D 89 PHE 0.046 0.003 PHE A 263 TYR 0.024 0.002 TYR B 291 ARG 0.005 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 71 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8736 (tp30) cc_final: 0.8376 (tp30) REVERT: A 157 LEU cc_start: 0.4904 (pp) cc_final: 0.4579 (pp) REVERT: B 132 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6467 (mt) REVERT: B 168 PHE cc_start: 0.4801 (OUTLIER) cc_final: 0.3360 (p90) REVERT: E 89 GLU cc_start: 0.8112 (pt0) cc_final: 0.7803 (pt0) REVERT: E 99 TYR cc_start: 0.3739 (OUTLIER) cc_final: 0.2446 (t80) REVERT: F 111 TYR cc_start: 0.5946 (OUTLIER) cc_final: 0.5064 (t80) REVERT: D 94 GLN cc_start: 0.5483 (OUTLIER) cc_final: 0.5213 (pt0) REVERT: G 108 ILE cc_start: 0.3156 (OUTLIER) cc_final: 0.2590 (pt) outliers start: 34 outliers final: 23 residues processed: 102 average time/residue: 0.1542 time to fit residues: 22.1896 Evaluate side-chains 99 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 70 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS G 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6522 Z= 0.172 Angle : 0.734 9.421 8871 Z= 0.362 Chirality : 0.046 0.421 1056 Planarity : 0.004 0.048 1106 Dihedral : 8.814 59.120 1212 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.19 % Rotamer: Outliers : 5.00 % Allowed : 27.19 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.12 (0.29), residues: 778 helix: -1.44 (0.45), residues: 117 sheet: -0.74 (0.37), residues: 181 loop : -1.72 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 59 HIS 0.003 0.001 HIS B 155 PHE 0.046 0.002 PHE A 263 TYR 0.016 0.001 TYR B 291 ARG 0.004 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8700 (tp30) cc_final: 0.8176 (tp30) REVERT: A 149 LYS cc_start: 0.8893 (tmtt) cc_final: 0.8495 (mmtt) REVERT: A 157 LEU cc_start: 0.4754 (pp) cc_final: 0.4459 (pp) REVERT: B 132 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6286 (mt) REVERT: B 168 PHE cc_start: 0.4599 (OUTLIER) cc_final: 0.3277 (p90) REVERT: E 72 ASP cc_start: 0.7940 (t0) cc_final: 0.7648 (t0) REVERT: E 89 GLU cc_start: 0.8118 (pt0) cc_final: 0.7855 (pt0) REVERT: E 99 TYR cc_start: 0.3702 (OUTLIER) cc_final: 0.2508 (t80) REVERT: F 111 TYR cc_start: 0.5748 (OUTLIER) cc_final: 0.4879 (t80) REVERT: D 94 GLN cc_start: 0.5027 (OUTLIER) cc_final: 0.4782 (pt0) REVERT: G 108 ILE cc_start: 0.2873 (OUTLIER) cc_final: 0.2358 (pt) outliers start: 32 outliers final: 20 residues processed: 108 average time/residue: 0.1505 time to fit residues: 22.7677 Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 0.0010 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN F 121 ASN D 89 HIS G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6522 Z= 0.297 Angle : 0.808 9.444 8871 Z= 0.408 Chirality : 0.048 0.430 1056 Planarity : 0.005 0.053 1106 Dihedral : 9.052 57.178 1212 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.25 % Favored : 90.62 % Rotamer: Outliers : 5.78 % Allowed : 26.25 % Favored : 67.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.28 (0.29), residues: 778 helix: -1.52 (0.46), residues: 110 sheet: -0.95 (0.36), residues: 183 loop : -1.79 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 59 HIS 0.006 0.001 HIS B 155 PHE 0.050 0.003 PHE A 263 TYR 0.025 0.002 TYR B 291 ARG 0.005 0.001 ARG F 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.769 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8801 (tp30) cc_final: 0.8289 (tp30) REVERT: B 132 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6471 (mt) REVERT: B 168 PHE cc_start: 0.4765 (OUTLIER) cc_final: 0.3272 (p90) REVERT: E 72 ASP cc_start: 0.7955 (t0) cc_final: 0.7745 (t0) REVERT: E 89 GLU cc_start: 0.8080 (pt0) cc_final: 0.7544 (pt0) REVERT: E 99 TYR cc_start: 0.3738 (OUTLIER) cc_final: 0.2385 (t80) REVERT: E 123 MET cc_start: 0.7349 (pmm) cc_final: 0.6777 (pmm) REVERT: F 111 TYR cc_start: 0.5964 (OUTLIER) cc_final: 0.5134 (t80) REVERT: D 94 GLN cc_start: 0.5355 (OUTLIER) cc_final: 0.5102 (pt0) REVERT: G 108 ILE cc_start: 0.2870 (OUTLIER) cc_final: 0.2305 (pt) outliers start: 37 outliers final: 26 residues processed: 104 average time/residue: 0.1562 time to fit residues: 22.8468 Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 70 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 144 GLN Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 54 TYR Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain X residue 44 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 61 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 37 optimal weight: 0.0370 chunk 49 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN B 155 HIS F 121 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6002 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6522 Z= 0.180 Angle : 0.767 9.896 8871 Z= 0.379 Chirality : 0.047 0.429 1056 Planarity : 0.004 0.048 1106 Dihedral : 8.814 56.233 1212 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.94 % Favored : 92.93 % Rotamer: Outliers : 4.69 % Allowed : 27.19 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.13 (0.29), residues: 778 helix: -1.44 (0.45), residues: 117 sheet: -0.80 (0.37), residues: 186 loop : -1.70 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 59 HIS 0.002 0.001 HIS B 155 PHE 0.049 0.002 PHE A 263 TYR 0.016 0.001 TYR B 291 ARG 0.004 0.001 ARG A 186 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 77 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8706 (tp30) cc_final: 0.8189 (tp30) REVERT: A 149 LYS cc_start: 0.8804 (tmtt) cc_final: 0.8490 (mmtt) REVERT: B 132 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6277 (mt) REVERT: B 155 HIS cc_start: 0.5836 (OUTLIER) cc_final: 0.5589 (p90) REVERT: B 168 PHE cc_start: 0.4395 (OUTLIER) cc_final: 0.3077 (p90) REVERT: E 72 ASP cc_start: 0.8016 (t0) cc_final: 0.7785 (t0) REVERT: E 81 HIS cc_start: 0.7435 (m-70) cc_final: 0.7131 (m-70) REVERT: E 99 TYR cc_start: 0.3650 (OUTLIER) cc_final: 0.2292 (t80) REVERT: F 111 TYR cc_start: 0.5788 (OUTLIER) cc_final: 0.4968 (t80) REVERT: D 94 GLN cc_start: 0.5028 (OUTLIER) cc_final: 0.4791 (pt0) REVERT: G 108 ILE cc_start: 0.2672 (OUTLIER) cc_final: 0.2036 (pt) REVERT: X 46 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8444 (mm) outliers start: 30 outliers final: 20 residues processed: 101 average time/residue: 0.1721 time to fit residues: 24.2280 Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain X residue 44 VAL Chi-restraints excluded: chain X residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 7 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 3 optimal weight: 0.0970 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS F 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.104604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.093644 restraints weight = 41068.500| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 6.55 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6266 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6522 Z= 0.182 Angle : 0.764 9.755 8871 Z= 0.376 Chirality : 0.046 0.424 1056 Planarity : 0.004 0.049 1106 Dihedral : 8.664 55.545 1212 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.84 % Favored : 92.03 % Rotamer: Outliers : 5.16 % Allowed : 27.19 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: -2.06 (0.29), residues: 778 helix: -1.33 (0.46), residues: 117 sheet: -0.70 (0.37), residues: 190 loop : -1.71 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 59 HIS 0.012 0.001 HIS B 155 PHE 0.049 0.002 PHE A 263 TYR 0.015 0.001 TYR B 291 ARG 0.006 0.001 ARG A 254 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1598.17 seconds wall clock time: 29 minutes 49.51 seconds (1789.51 seconds total)