Starting phenix.real_space_refine on Tue Feb 11 17:48:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw4_41658/02_2025/8tw4_41658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw4_41658/02_2025/8tw4_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_41658/02_2025/8tw4_41658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw4_41658/02_2025/8tw4_41658.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw4_41658/02_2025/8tw4_41658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw4_41658/02_2025/8tw4_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-5592/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: 5.04, per 1000 atoms: 0.79 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: 1.75 Conformation dependent library (CDL) restraints added in 965.6 milliseconds 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: 0.79 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: 1.78 Time building geometry restraints manager: 2.00 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: 2.430 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.370 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.390 ------------------------------------------------------------------------------- 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 : 0.683 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: 0.1966 time to fit residues: 27.3731 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 : 0.777 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.108829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.098005 restraints weight = 40027.269| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 6.65 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 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 : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8700 (tmtt) cc_final: 0.8484 (mmtt) REVERT: B 38 MET cc_start: 0.6653 (tpp) cc_final: 0.5930 (tpp) REVERT: B 155 HIS cc_start: 0.6818 (OUTLIER) cc_final: 0.6492 (p-80) REVERT: B 168 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.3322 (p90) REVERT: E 59 TRP cc_start: 0.6686 (m100) cc_final: 0.6451 (m100) REVERT: E 89 GLU cc_start: 0.7989 (pt0) cc_final: 0.7719 (pt0) REVERT: F 111 TYR cc_start: 0.5456 (OUTLIER) cc_final: 0.4153 (t80) REVERT: D 92 MET cc_start: 0.4288 (mmm) cc_final: 0.3939 (mmm) REVERT: D 94 GLN cc_start: 0.5252 (OUTLIER) cc_final: 0.4345 (pm20) outliers start: 38 outliers final: 19 residues processed: 107 average time/residue: 0.1617 time to fit residues: 23.5295 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 : 0.730 ------------------------------------------------------------------------------- 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 66 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 0.0270 chunk 53 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 48 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.106990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.095645 restraints weight = 41406.817| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 7.09 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 moved from start: 0.1823 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= 0.229 Angle : 0.755 9.492 8871 Z= 0.381 Chirality : 0.046 0.413 1056 Planarity : 0.005 0.052 1106 Dihedral : 9.356 57.393 1218 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.67 % Rotamer: Outliers : 5.62 % Allowed : 21.25 % Favored : 73.12 % 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: -2.19 (0.28), residues: 778 helix: -1.56 (0.44), residues: 116 sheet: -0.32 (0.37), residues: 173 loop : -1.94 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 241 HIS 0.003 0.001 HIS B 225 PHE 0.043 0.002 PHE Y 40 TYR 0.023 0.002 TYR B 291 ARG 0.005 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 115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8897 (tp30) cc_final: 0.8400 (tp30) REVERT: A 87 LYS cc_start: 0.6950 (ptpt) cc_final: 0.6317 (tptt) REVERT: B 38 MET cc_start: 0.6917 (tpp) cc_final: 0.6163 (tpp) REVERT: B 155 HIS cc_start: 0.6780 (OUTLIER) cc_final: 0.6498 (p-80) REVERT: B 168 PHE cc_start: 0.4483 (OUTLIER) cc_final: 0.3040 (p90) REVERT: E 89 GLU cc_start: 0.7919 (pt0) cc_final: 0.7657 (pt0) REVERT: E 99 TYR cc_start: 0.3924 (OUTLIER) cc_final: 0.3304 (t80) REVERT: E 125 MET cc_start: 0.6566 (pmm) cc_final: 0.6245 (pmm) REVERT: F 111 TYR cc_start: 0.5670 (OUTLIER) cc_final: 0.4488 (t80) REVERT: D 30 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6761 (pm20) REVERT: D 92 MET cc_start: 0.4955 (mmm) cc_final: 0.4539 (mmm) REVERT: D 94 GLN cc_start: 0.5151 (OUTLIER) cc_final: 0.4283 (pm20) outliers start: 36 outliers final: 21 residues processed: 107 average time/residue: 0.1852 time to fit residues: 26.6191 Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.8980 chunk 38 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.105788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.094737 restraints weight = 42099.844| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 6.91 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6522 Z= 0.234 Angle : 0.747 9.865 8871 Z= 0.378 Chirality : 0.046 0.419 1056 Planarity : 0.004 0.050 1106 Dihedral : 9.236 56.787 1216 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.67 % Rotamer: Outliers : 5.16 % Allowed : 22.66 % Favored : 72.19 % 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: -2.19 (0.28), residues: 778 helix: -1.54 (0.43), residues: 116 sheet: -0.42 (0.38), residues: 170 loop : -1.89 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 PHE 0.033 0.002 PHE Y 40 TYR 0.023 0.002 TYR B 291 ARG 0.005 0.001 ARG A 186 *********************** 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 113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8995 (tp30) cc_final: 0.8733 (tp30) REVERT: A 149 LYS cc_start: 0.8712 (tmtt) cc_final: 0.8493 (mmtt) REVERT: B 155 HIS cc_start: 0.6730 (OUTLIER) cc_final: 0.6429 (p-80) REVERT: B 168 PHE cc_start: 0.4806 (OUTLIER) cc_final: 0.3406 (p90) REVERT: E 72 ASP cc_start: 0.7948 (t0) cc_final: 0.7716 (t0) REVERT: E 89 GLU cc_start: 0.7818 (pt0) cc_final: 0.7552 (pt0) REVERT: E 99 TYR cc_start: 0.4244 (OUTLIER) cc_final: 0.3143 (t80) REVERT: E 125 MET cc_start: 0.6271 (pmm) cc_final: 0.6026 (pmm) REVERT: F 111 TYR cc_start: 0.5673 (OUTLIER) cc_final: 0.4497 (t80) REVERT: D 30 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6755 (pt0) REVERT: D 80 LYS cc_start: 0.7477 (tptt) cc_final: 0.7166 (tptt) REVERT: D 92 MET cc_start: 0.5254 (mmm) cc_final: 0.4735 (mmt) REVERT: G 108 ILE cc_start: 0.5193 (OUTLIER) cc_final: 0.4628 (pt) outliers start: 33 outliers final: 23 residues processed: 107 average time/residue: 0.1692 time to fit residues: 24.6078 Evaluate side-chains 101 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 72 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 55 optimal weight: 0.0000 chunk 26 optimal weight: 3.9990 chunk 15 optimal weight: 0.0050 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.107189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.096115 restraints weight = 41886.023| |-----------------------------------------------------------------------------| r_work (start): 0.4262 rms_B_bonded: 7.00 r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6522 Z= 0.171 Angle : 0.716 10.039 8871 Z= 0.358 Chirality : 0.045 0.408 1056 Planarity : 0.004 0.047 1106 Dihedral : 8.990 57.039 1216 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.44 % Rotamer: Outliers : 4.69 % Allowed : 24.22 % Favored : 71.09 % 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: -1.56 (0.44), residues: 117 sheet: -0.46 (0.39), residues: 167 loop : -1.84 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 55 HIS 0.002 0.001 HIS B 225 PHE 0.043 0.002 PHE A 263 TYR 0.017 0.001 TYR B 291 ARG 0.005 0.000 ARG A 186 *********************** 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 109 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8930 (tp30) cc_final: 0.8649 (tp30) REVERT: B 109 PHE cc_start: 0.8392 (m-80) cc_final: 0.8192 (m-10) REVERT: B 155 HIS cc_start: 0.6440 (OUTLIER) cc_final: 0.6233 (p-80) REVERT: B 168 PHE cc_start: 0.4372 (OUTLIER) cc_final: 0.3178 (p90) REVERT: E 72 ASP cc_start: 0.7532 (t0) cc_final: 0.7174 (t0) REVERT: E 89 GLU cc_start: 0.8143 (pt0) cc_final: 0.7813 (pt0) REVERT: E 99 TYR cc_start: 0.3961 (OUTLIER) cc_final: 0.2902 (t80) REVERT: F 111 TYR cc_start: 0.5591 (OUTLIER) cc_final: 0.4500 (t80) REVERT: Y 38 ILE cc_start: 0.8144 (mt) cc_final: 0.7622 (tt) outliers start: 30 outliers final: 20 residues processed: 102 average time/residue: 0.1571 time to fit residues: 22.3743 Evaluate side-chains 98 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 130 ILE 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 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.0970 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 61 optimal weight: 0.0370 chunk 5 optimal weight: 3.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.107260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.096237 restraints weight = 41634.374| |-----------------------------------------------------------------------------| r_work (start): 0.4268 rms_B_bonded: 6.92 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6522 Z= 0.159 Angle : 0.696 9.432 8871 Z= 0.348 Chirality : 0.045 0.404 1056 Planarity : 0.004 0.046 1106 Dihedral : 8.765 59.359 1216 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.56 % Favored : 93.32 % Rotamer: Outliers : 4.53 % Allowed : 25.78 % 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: -2.07 (0.29), residues: 778 helix: -1.50 (0.44), residues: 117 sheet: -0.39 (0.40), residues: 162 loop : -1.77 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 53 HIS 0.002 0.001 HIS B 225 PHE 0.044 0.002 PHE A 263 TYR 0.017 0.001 TYR B 291 ARG 0.007 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 106 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8912 (tp30) cc_final: 0.8632 (tp30) REVERT: A 157 LEU cc_start: 0.5284 (tp) cc_final: 0.4951 (tp) REVERT: B 46 MET cc_start: 0.7049 (mtt) cc_final: 0.6759 (mpp) REVERT: B 168 PHE cc_start: 0.4407 (OUTLIER) cc_final: 0.3221 (p90) REVERT: E 72 ASP cc_start: 0.7478 (t0) cc_final: 0.7100 (t0) REVERT: E 89 GLU cc_start: 0.8103 (pt0) cc_final: 0.7863 (pt0) REVERT: E 99 TYR cc_start: 0.3824 (OUTLIER) cc_final: 0.2638 (t80) REVERT: F 111 TYR cc_start: 0.5648 (OUTLIER) cc_final: 0.4577 (t80) REVERT: D 94 GLN cc_start: 0.5400 (OUTLIER) cc_final: 0.5081 (pt0) REVERT: G 84 MET cc_start: 0.4381 (tmm) cc_final: 0.3899 (tmm) REVERT: G 108 ILE cc_start: 0.4607 (OUTLIER) cc_final: 0.4063 (pt) REVERT: Y 38 ILE cc_start: 0.8228 (mt) cc_final: 0.7691 (tt) outliers start: 29 outliers final: 19 residues processed: 102 average time/residue: 0.1537 time to fit residues: 22.1364 Evaluate side-chains 98 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 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 212 LEU 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 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 75 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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** D 89 HIS G 73 ASN ** G 86 GLN ** 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 = 0.4404 r_free = 0.4404 target = 0.102000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.090931 restraints weight = 42087.700| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 6.74 r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6343 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6522 Z= 0.320 Angle : 0.814 10.060 8871 Z= 0.411 Chirality : 0.048 0.425 1056 Planarity : 0.005 0.055 1106 Dihedral : 9.270 59.574 1214 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.38 % Favored : 90.49 % Rotamer: Outliers : 5.78 % Allowed : 25.16 % Favored : 69.06 % 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: -2.34 (0.28), residues: 778 helix: -2.07 (0.39), residues: 117 sheet: -0.71 (0.38), residues: 170 loop : -1.80 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 59 HIS 0.008 0.002 HIS B 155 PHE 0.045 0.004 PHE A 263 TYR 0.025 0.002 TYR B 291 ARG 0.009 0.001 ARG D 72 *********************** 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 109 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9071 (tp30) cc_final: 0.8839 (tp30) REVERT: A 157 LEU cc_start: 0.5469 (tp) cc_final: 0.5151 (tp) REVERT: B 132 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6670 (mt) REVERT: B 168 PHE cc_start: 0.4935 (OUTLIER) cc_final: 0.3448 (p90) REVERT: E 72 ASP cc_start: 0.7525 (t0) cc_final: 0.7191 (t0) REVERT: E 89 GLU cc_start: 0.7924 (pt0) cc_final: 0.7612 (pt0) REVERT: E 99 TYR cc_start: 0.4109 (OUTLIER) cc_final: 0.2857 (t80) REVERT: F 111 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.5024 (t80) REVERT: G 84 MET cc_start: 0.4561 (tmm) cc_final: 0.4195 (tmm) REVERT: G 108 ILE cc_start: 0.4920 (OUTLIER) cc_final: 0.4356 (pt) outliers start: 37 outliers final: 27 residues processed: 104 average time/residue: 0.1538 time to fit residues: 22.9856 Evaluate side-chains 103 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 71 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 188 MET 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 191 ASP 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 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 41 ILE 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 76 SER 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 22 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.0870 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.103315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.092201 restraints weight = 42513.361| |-----------------------------------------------------------------------------| r_work (start): 0.4209 rms_B_bonded: 6.92 r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6522 Z= 0.221 Angle : 0.749 9.479 8871 Z= 0.375 Chirality : 0.047 0.427 1056 Planarity : 0.004 0.046 1106 Dihedral : 8.999 59.280 1214 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.29 % Rotamer: Outliers : 5.31 % Allowed : 25.62 % Favored : 69.06 % 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: -2.20 (0.29), residues: 778 helix: -1.56 (0.43), residues: 117 sheet: -0.76 (0.36), residues: 182 loop : -1.77 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 59 HIS 0.003 0.001 HIS B 155 PHE 0.044 0.003 PHE A 263 TYR 0.021 0.002 TYR B 291 ARG 0.004 0.001 ARG D 72 *********************** 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 107 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9041 (tp30) cc_final: 0.8450 (tp30) REVERT: A 149 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8457 (mmtt) REVERT: B 132 LEU cc_start: 0.6809 (OUTLIER) cc_final: 0.6459 (mt) REVERT: B 168 PHE cc_start: 0.4724 (OUTLIER) cc_final: 0.3349 (p90) REVERT: E 72 ASP cc_start: 0.7287 (t0) cc_final: 0.6909 (t0) REVERT: E 89 GLU cc_start: 0.8076 (pt0) cc_final: 0.7503 (pt0) REVERT: E 99 TYR cc_start: 0.3676 (OUTLIER) cc_final: 0.2541 (t80) REVERT: E 137 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8252 (p0) REVERT: F 111 TYR cc_start: 0.5897 (OUTLIER) cc_final: 0.4961 (t80) REVERT: G 84 MET cc_start: 0.4528 (tmm) cc_final: 0.4293 (tmm) REVERT: G 108 ILE cc_start: 0.4482 (OUTLIER) cc_final: 0.3897 (pt) outliers start: 34 outliers final: 24 residues processed: 100 average time/residue: 0.1704 time to fit residues: 24.2049 Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 188 MET 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 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 41 ILE 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.105159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.094483 restraints weight = 42690.718| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 6.79 r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6209 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6522 Z= 0.172 Angle : 0.725 9.409 8871 Z= 0.357 Chirality : 0.046 0.417 1056 Planarity : 0.004 0.046 1106 Dihedral : 8.649 59.587 1214 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.56 % Favored : 93.32 % Rotamer: Outliers : 4.22 % Allowed : 26.88 % Favored : 68.91 % 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: -2.04 (0.29), residues: 778 helix: -1.34 (0.45), residues: 117 sheet: -0.69 (0.36), residues: 191 loop : -1.69 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 59 HIS 0.002 0.001 HIS B 225 PHE 0.044 0.002 PHE A 263 TYR 0.014 0.001 TYR B 281 ARG 0.005 0.001 ARG D 72 *********************** 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 105 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9023 (tp30) cc_final: 0.8439 (tp30) REVERT: A 149 LYS cc_start: 0.8675 (tmtt) cc_final: 0.8455 (mmtt) REVERT: B 132 LEU cc_start: 0.6710 (OUTLIER) cc_final: 0.6418 (mt) REVERT: B 168 PHE cc_start: 0.4324 (OUTLIER) cc_final: 0.3126 (p90) REVERT: E 72 ASP cc_start: 0.7430 (t0) cc_final: 0.7115 (t0) REVERT: E 99 TYR cc_start: 0.3619 (OUTLIER) cc_final: 0.2364 (t80) REVERT: E 125 MET cc_start: 0.6366 (pmm) cc_final: 0.6159 (pmm) REVERT: E 137 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8053 (p0) REVERT: F 111 TYR cc_start: 0.5667 (OUTLIER) cc_final: 0.4814 (t80) REVERT: G 108 ILE cc_start: 0.4466 (OUTLIER) cc_final: 0.3810 (pt) outliers start: 27 outliers final: 17 residues processed: 98 average time/residue: 0.1445 time to fit residues: 20.2862 Evaluate side-chains 97 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 74 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 188 MET 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 168 PHE Chi-restraints excluded: chain B residue 212 LEU 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 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 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 112 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.103316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.092435 restraints weight = 43647.312| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 6.87 r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6522 Z= 0.218 Angle : 0.748 9.366 8871 Z= 0.372 Chirality : 0.046 0.421 1056 Planarity : 0.004 0.047 1106 Dihedral : 8.618 57.685 1213 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.46 % Favored : 92.42 % Rotamer: Outliers : 4.22 % Allowed : 27.03 % Favored : 68.75 % 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: -2.00 (0.29), residues: 778 helix: -1.30 (0.45), residues: 117 sheet: -0.66 (0.37), residues: 183 loop : -1.65 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 59 HIS 0.003 0.001 HIS B 155 PHE 0.048 0.003 PHE A 263 TYR 0.017 0.001 TYR B 291 ARG 0.010 0.001 ARG E 117 ********************** 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 101 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 74 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9029 (tp30) cc_final: 0.8445 (tp30) REVERT: B 132 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6427 (mt) REVERT: B 168 PHE cc_start: 0.4629 (OUTLIER) cc_final: 0.3349 (p90) REVERT: E 99 TYR cc_start: 0.3656 (OUTLIER) cc_final: 0.2258 (t80) REVERT: E 123 MET cc_start: 0.7000 (pmm) cc_final: 0.6405 (pmm) REVERT: E 125 MET cc_start: 0.6470 (pmm) cc_final: 0.6225 (pmm) REVERT: F 111 TYR cc_start: 0.5712 (OUTLIER) cc_final: 0.4849 (t80) REVERT: G 108 ILE cc_start: 0.4880 (OUTLIER) cc_final: 0.4340 (pt) outliers start: 27 outliers final: 20 residues processed: 97 average time/residue: 0.1590 time to fit residues: 22.1464 Evaluate side-chains 99 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 188 MET 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 168 PHE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU 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 137 ASP 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 112 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 115 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.104383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.093574 restraints weight = 43914.125| |-----------------------------------------------------------------------------| r_work (start): 0.4243 rms_B_bonded: 6.92 r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6522 Z= 0.186 Angle : 0.751 11.621 8871 Z= 0.367 Chirality : 0.046 0.420 1056 Planarity : 0.004 0.046 1106 Dihedral : 8.527 57.396 1213 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 4.06 % Allowed : 27.03 % Favored : 68.91 % 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: -1.96 (0.29), residues: 778 helix: -1.23 (0.45), residues: 117 sheet: -0.66 (0.36), residues: 195 loop : -1.65 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 59 HIS 0.002 0.001 HIS B 225 PHE 0.049 0.002 PHE A 263 TYR 0.015 0.001 TYR B 291 ARG 0.009 0.001 ARG E 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3227.15 seconds wall clock time: 58 minutes 8.96 seconds (3488.96 seconds total)