Starting phenix.real_space_refine on Fri Aug 22 17:22:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw4_41658/08_2025/8tw4_41658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw4_41658/08_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_41658/08_2025/8tw4_41658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw4_41658/08_2025/8tw4_41658.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw4_41658/08_2025/8tw4_41658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw4_41658/08_2025/8tw4_41658.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ARG:plan': 2, 'ASP:plan': 1, 'TYR: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: {'GLU:plan': 4, 'HIS:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 1, '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: {'ASP:plan': 3, 'GLU:plan': 2} 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, 'ASP:plan': 1, 'TYR: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: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU: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: 1.77, per 1000 atoms: 0.28 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: 0.59 Conformation dependent library (CDL) restraints added in 366.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.14 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: 0.77 Time building geometry restraints manager: 0.76 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: 1.800 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.430 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.580 ------------------------------------------------------------------------------- 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 6544 Z= 0.199 Angle : 0.924 17.520 8924 Z= 0.466 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.001 ARG E 117 TYR 0.019 0.002 TYR B 291 PHE 0.030 0.002 PHE G 118 TRP 0.026 0.002 TRP E 59 HIS 0.003 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 6522) covalent geometry : angle 0.86194 ( 8871) SS BOND : bond 0.00532 ( 13) SS BOND : angle 1.37992 ( 26) hydrogen bonds : bond 0.25265 ( 184) hydrogen bonds : angle 10.14051 ( 462) link_BETA1-4 : bond 0.01466 ( 4) link_BETA1-4 : angle 4.56619 ( 12) link_NAG-ASN : bond 0.01116 ( 5) link_NAG-ASN : angle 6.97038 ( 15) *********************** 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 : 0.251 Fit side-chains revert: symmetry clash 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: 0.0876 time to fit residues: 12.2865 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 : 0.256 ------------------------------------------------------------------------------- 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 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.0980 chunk 74 optimal weight: 0.6980 overall best weight: 0.2978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 HIS G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4561 r_free = 0.4561 target = 0.112328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.101237 restraints weight = 39897.638| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 6.80 r_work (final): 0.4349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5994 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6544 Z= 0.135 Angle : 0.814 13.230 8924 Z= 0.389 Chirality : 0.046 0.407 1056 Planarity : 0.004 0.044 1106 Dihedral : 9.901 56.832 1237 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 15.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.17 % Favored : 93.70 % Rotamer: Outliers : 4.53 % Allowed : 21.41 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.28), residues: 778 helix: -1.54 (0.41), residues: 124 sheet: -0.19 (0.37), residues: 180 loop : -1.89 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 213 TYR 0.014 0.001 TYR B 291 PHE 0.027 0.002 PHE G 120 TRP 0.016 0.002 TRP E 59 HIS 0.003 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 6522) covalent geometry : angle 0.76626 ( 8871) SS BOND : bond 0.00282 ( 13) SS BOND : angle 0.76402 ( 26) hydrogen bonds : bond 0.04405 ( 184) hydrogen bonds : angle 7.52273 ( 462) link_BETA1-4 : bond 0.01059 ( 4) link_BETA1-4 : angle 3.52003 ( 12) link_NAG-ASN : bond 0.00908 ( 5) link_NAG-ASN : angle 6.02131 ( 15) *********************** 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 114 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.151 Fit side-chains REVERT: A 87 LYS cc_start: 0.6665 (ptpt) cc_final: 0.6162 (mmtm) REVERT: B 38 MET cc_start: 0.6613 (tpp) cc_final: 0.6016 (tpp) REVERT: B 155 HIS cc_start: 0.6538 (OUTLIER) cc_final: 0.6284 (p-80) REVERT: B 168 PHE cc_start: 0.4296 (OUTLIER) cc_final: 0.3087 (p90) REVERT: E 59 TRP cc_start: 0.6645 (m100) cc_final: 0.6386 (m100) REVERT: E 101 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7687 (mtt-85) REVERT: E 125 MET cc_start: 0.6496 (pmm) cc_final: 0.6113 (pmm) REVERT: D 80 LYS cc_start: 0.7301 (tptp) cc_final: 0.6865 (tptp) REVERT: D 94 GLN cc_start: 0.4981 (OUTLIER) cc_final: 0.4237 (pm20) outliers start: 29 outliers final: 12 residues processed: 104 average time/residue: 0.0593 time to fit residues: 8.6682 Evaluate side-chains 94 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR 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 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 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 Y residue 40 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.4506 r_free = 0.4506 target = 0.109085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.097848 restraints weight = 41123.608| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 7.02 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6544 Z= 0.145 Angle : 0.771 12.517 8924 Z= 0.372 Chirality : 0.046 0.403 1056 Planarity : 0.004 0.048 1106 Dihedral : 9.167 58.499 1216 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.81 % Favored : 93.06 % Rotamer: Outliers : 4.38 % Allowed : 22.19 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.28), residues: 778 helix: -1.25 (0.44), residues: 121 sheet: -0.04 (0.38), residues: 167 loop : -1.85 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 117 TYR 0.018 0.001 TYR B 291 PHE 0.019 0.002 PHE G 120 TRP 0.012 0.002 TRP E 59 HIS 0.002 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 6522) covalent geometry : angle 0.72632 ( 8871) SS BOND : bond 0.00366 ( 13) SS BOND : angle 0.95657 ( 26) hydrogen bonds : bond 0.03863 ( 184) hydrogen bonds : angle 7.12743 ( 462) link_BETA1-4 : bond 0.00649 ( 4) link_BETA1-4 : angle 2.90947 ( 12) link_NAG-ASN : bond 0.00833 ( 5) link_NAG-ASN : angle 5.75934 ( 15) *********************** 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 110 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 87 LYS cc_start: 0.6843 (ptpt) cc_final: 0.6281 (mmtm) REVERT: B 38 MET cc_start: 0.6869 (tpp) cc_final: 0.6073 (tpp) REVERT: B 155 HIS cc_start: 0.6536 (OUTLIER) cc_final: 0.6281 (p-80) REVERT: B 168 PHE cc_start: 0.4650 (OUTLIER) cc_final: 0.3348 (p90) REVERT: E 99 TYR cc_start: 0.3732 (OUTLIER) cc_final: 0.3051 (t80) REVERT: F 111 TYR cc_start: 0.5524 (OUTLIER) cc_final: 0.4365 (t80) outliers start: 28 outliers final: 16 residues processed: 103 average time/residue: 0.0640 time to fit residues: 9.2122 Evaluate side-chains 98 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 155 HIS 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 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 112 VAL Chi-restraints excluded: chain Y residue 40 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 58 optimal weight: 10.0000 chunk 74 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 71 optimal weight: 0.0270 chunk 45 optimal weight: 9.9990 overall best weight: 2.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 212 ASN ** 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 = 0.4434 r_free = 0.4434 target = 0.104372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.093282 restraints weight = 42399.506| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 6.89 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6274 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6544 Z= 0.215 Angle : 0.822 11.773 8924 Z= 0.405 Chirality : 0.048 0.476 1056 Planarity : 0.005 0.054 1106 Dihedral : 9.457 59.553 1216 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.84 % Favored : 92.03 % Rotamer: Outliers : 5.78 % Allowed : 22.34 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.28), residues: 778 helix: -1.46 (0.43), residues: 117 sheet: -0.43 (0.38), residues: 168 loop : -1.88 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 117 TYR 0.021 0.002 TYR B 291 PHE 0.046 0.003 PHE A 263 TRP 0.018 0.002 TRP G 55 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 6522) covalent geometry : angle 0.78121 ( 8871) SS BOND : bond 0.00574 ( 13) SS BOND : angle 1.23471 ( 26) hydrogen bonds : bond 0.04137 ( 184) hydrogen bonds : angle 7.42239 ( 462) link_BETA1-4 : bond 0.00589 ( 4) link_BETA1-4 : angle 3.10043 ( 12) link_NAG-ASN : bond 0.00893 ( 5) link_NAG-ASN : angle 5.55513 ( 15) *********************** 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 115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 78 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9051 (tp30) cc_final: 0.8792 (tp30) REVERT: A 149 LYS cc_start: 0.8692 (tmtt) cc_final: 0.8436 (mmtt) REVERT: B 155 HIS cc_start: 0.6785 (OUTLIER) cc_final: 0.6441 (p-80) REVERT: B 168 PHE cc_start: 0.4970 (OUTLIER) cc_final: 0.3431 (p90) REVERT: E 72 ASP cc_start: 0.7983 (t0) cc_final: 0.7696 (t0) REVERT: E 99 TYR cc_start: 0.4502 (OUTLIER) cc_final: 0.3025 (t80) REVERT: E 125 MET cc_start: 0.6624 (pmm) cc_final: 0.6199 (pmm) REVERT: F 111 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.4700 (t80) REVERT: D 80 LYS cc_start: 0.7393 (tptt) cc_final: 0.6983 (tptt) REVERT: D 92 MET cc_start: 0.4971 (tpt) cc_final: 0.4550 (tpt) outliers start: 37 outliers final: 25 residues processed: 107 average time/residue: 0.0710 time to fit residues: 10.3349 Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE 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 155 HIS 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** 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 = 0.4435 r_free = 0.4435 target = 0.104082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.092993 restraints weight = 42938.240| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 6.96 r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6289 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6544 Z= 0.180 Angle : 0.791 11.192 8924 Z= 0.388 Chirality : 0.047 0.449 1056 Planarity : 0.005 0.051 1106 Dihedral : 9.254 57.835 1214 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 5.47 % Allowed : 24.22 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.28), residues: 778 helix: -1.49 (0.43), residues: 117 sheet: -0.61 (0.37), residues: 179 loop : -1.86 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 186 TYR 0.020 0.002 TYR B 291 PHE 0.043 0.003 PHE A 263 TRP 0.018 0.002 TRP E 59 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 6522) covalent geometry : angle 0.75026 ( 8871) SS BOND : bond 0.00523 ( 13) SS BOND : angle 1.16138 ( 26) hydrogen bonds : bond 0.03898 ( 184) hydrogen bonds : angle 7.11502 ( 462) link_BETA1-4 : bond 0.00376 ( 4) link_BETA1-4 : angle 3.00929 ( 12) link_NAG-ASN : bond 0.00834 ( 5) link_NAG-ASN : angle 5.43351 ( 15) *********************** 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 113 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 78 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9092 (tp30) cc_final: 0.8854 (tp30) REVERT: B 38 MET cc_start: 0.7366 (tpp) cc_final: 0.7162 (tpp) REVERT: B 155 HIS cc_start: 0.6550 (OUTLIER) cc_final: 0.6267 (p-80) REVERT: B 168 PHE cc_start: 0.4777 (OUTLIER) cc_final: 0.3358 (p90) REVERT: E 72 ASP cc_start: 0.7662 (t0) cc_final: 0.7304 (t0) REVERT: E 99 TYR cc_start: 0.3678 (OUTLIER) cc_final: 0.2825 (t80) REVERT: F 111 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.4800 (t80) REVERT: D 80 LYS cc_start: 0.7568 (tptt) cc_final: 0.7133 (tptt) REVERT: D 94 GLN cc_start: 0.5244 (OUTLIER) cc_final: 0.4893 (pt0) REVERT: G 84 MET cc_start: 0.4499 (tmm) cc_final: 0.4290 (tmm) REVERT: G 108 ILE cc_start: 0.4831 (OUTLIER) cc_final: 0.4244 (pt) outliers start: 35 outliers final: 23 residues processed: 107 average time/residue: 0.0676 time to fit residues: 9.9132 Evaluate side-chains 100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 71 time to evaluate : 0.222 ------------------------------------------------------------------------------- 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 191 LYS 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 25 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 30 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN 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 = 0.4431 r_free = 0.4431 target = 0.103534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.092666 restraints weight = 43162.398| |-----------------------------------------------------------------------------| r_work (start): 0.4215 rms_B_bonded: 6.91 r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6544 Z= 0.154 Angle : 0.781 10.843 8924 Z= 0.381 Chirality : 0.046 0.445 1056 Planarity : 0.004 0.048 1106 Dihedral : 9.134 59.483 1214 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.29 % Rotamer: Outliers : 4.69 % Allowed : 26.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.29), residues: 778 helix: -1.43 (0.44), residues: 117 sheet: -0.66 (0.38), residues: 173 loop : -1.81 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 186 TYR 0.018 0.002 TYR B 291 PHE 0.044 0.003 PHE A 263 TRP 0.017 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6522) covalent geometry : angle 0.74187 ( 8871) SS BOND : bond 0.00458 ( 13) SS BOND : angle 1.08513 ( 26) hydrogen bonds : bond 0.03844 ( 184) hydrogen bonds : angle 7.03901 ( 462) link_BETA1-4 : bond 0.00471 ( 4) link_BETA1-4 : angle 3.02134 ( 12) link_NAG-ASN : bond 0.00832 ( 5) link_NAG-ASN : angle 5.30678 ( 15) *********************** 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 109 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9078 (tp30) cc_final: 0.8473 (tp30) REVERT: A 149 LYS cc_start: 0.8775 (tmtt) cc_final: 0.8473 (mmtt) REVERT: B 155 HIS cc_start: 0.6455 (OUTLIER) cc_final: 0.6237 (p-80) REVERT: B 168 PHE cc_start: 0.4737 (OUTLIER) cc_final: 0.3412 (p90) REVERT: E 72 ASP cc_start: 0.7714 (t0) cc_final: 0.7351 (t0) REVERT: E 99 TYR cc_start: 0.3820 (OUTLIER) cc_final: 0.2676 (t80) REVERT: E 125 MET cc_start: 0.6668 (pmm) cc_final: 0.6465 (pmm) REVERT: F 111 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.4853 (t80) REVERT: D 80 LYS cc_start: 0.7521 (tptt) cc_final: 0.7043 (tptt) REVERT: D 94 GLN cc_start: 0.5118 (OUTLIER) cc_final: 0.4776 (pt0) REVERT: G 108 ILE cc_start: 0.4694 (OUTLIER) cc_final: 0.4129 (pt) outliers start: 30 outliers final: 21 residues processed: 106 average time/residue: 0.0594 time to fit residues: 8.8925 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 : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP 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 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 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 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 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 59 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 29 optimal weight: 0.0970 chunk 26 optimal weight: 7.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN F 121 ASN G 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.104857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.093858 restraints weight = 42769.726| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 7.06 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.3295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6544 Z= 0.132 Angle : 0.831 25.966 8924 Z= 0.386 Chirality : 0.047 0.425 1056 Planarity : 0.004 0.047 1106 Dihedral : 8.878 59.757 1214 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 5.78 % Allowed : 26.41 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.29), residues: 778 helix: -1.38 (0.45), residues: 117 sheet: -0.55 (0.37), residues: 178 loop : -1.79 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 101 TYR 0.014 0.001 TYR B 281 PHE 0.045 0.002 PHE A 263 TRP 0.019 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 6522) covalent geometry : angle 0.73783 ( 8871) SS BOND : bond 0.00338 ( 13) SS BOND : angle 0.93621 ( 26) hydrogen bonds : bond 0.03623 ( 184) hydrogen bonds : angle 6.75213 ( 462) link_BETA1-4 : bond 0.01502 ( 4) link_BETA1-4 : angle 3.52250 ( 12) link_NAG-ASN : bond 0.00657 ( 5) link_NAG-ASN : angle 8.82469 ( 15) *********************** 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 118 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 81 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9100 (tp30) cc_final: 0.8522 (tp30) REVERT: A 149 LYS cc_start: 0.8754 (tmtt) cc_final: 0.8466 (mmtt) REVERT: B 168 PHE cc_start: 0.4666 (OUTLIER) cc_final: 0.3362 (p90) REVERT: B 285 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7393 (mm) REVERT: E 72 ASP cc_start: 0.7703 (t0) cc_final: 0.7355 (t0) REVERT: E 99 TYR cc_start: 0.3589 (OUTLIER) cc_final: 0.2578 (t80) REVERT: E 125 MET cc_start: 0.6409 (pmm) cc_final: 0.6165 (pmm) REVERT: E 137 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8297 (p0) REVERT: F 111 TYR cc_start: 0.5647 (OUTLIER) cc_final: 0.4705 (t80) REVERT: D 30 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6224 (pt0) REVERT: D 80 LYS cc_start: 0.7570 (tptt) cc_final: 0.7163 (tptt) REVERT: D 94 GLN cc_start: 0.5256 (OUTLIER) cc_final: 0.4878 (pt0) REVERT: G 86 GLN cc_start: 0.2231 (OUTLIER) cc_final: 0.1729 (pm20) REVERT: G 108 ILE cc_start: 0.4385 (OUTLIER) cc_final: 0.3799 (pt) outliers start: 37 outliers final: 20 residues processed: 113 average time/residue: 0.0571 time to fit residues: 9.0895 Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 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 285 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 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 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 86 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 29 optimal weight: 0.0030 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 = 0.4452 r_free = 0.4452 target = 0.104599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.093838 restraints weight = 43152.466| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 6.91 r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6231 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6544 Z= 0.144 Angle : 0.819 22.607 8924 Z= 0.386 Chirality : 0.047 0.425 1056 Planarity : 0.004 0.047 1106 Dihedral : 8.786 59.824 1214 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.81 % Favored : 93.06 % Rotamer: Outliers : 4.53 % Allowed : 27.19 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.29), residues: 778 helix: -1.41 (0.45), residues: 117 sheet: -0.44 (0.38), residues: 180 loop : -1.77 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 101 TYR 0.016 0.001 TYR B 291 PHE 0.050 0.003 PHE A 263 TRP 0.030 0.002 TRP E 59 HIS 0.004 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6522) covalent geometry : angle 0.73828 ( 8871) SS BOND : bond 0.00385 ( 13) SS BOND : angle 1.01180 ( 26) hydrogen bonds : bond 0.03711 ( 184) hydrogen bonds : angle 6.71648 ( 462) link_BETA1-4 : bond 0.01112 ( 4) link_BETA1-4 : angle 3.35784 ( 12) link_NAG-ASN : bond 0.00735 ( 5) link_NAG-ASN : angle 8.09655 ( 15) *********************** 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: 29 poor density : 78 time to evaluate : 0.181 Fit side-chains revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9019 (tp30) cc_final: 0.8420 (tp30) REVERT: B 168 PHE cc_start: 0.4575 (OUTLIER) cc_final: 0.3330 (p90) REVERT: E 72 ASP cc_start: 0.7592 (t0) cc_final: 0.7238 (t0) REVERT: E 99 TYR cc_start: 0.3664 (OUTLIER) cc_final: 0.2502 (t80) REVERT: E 137 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8160 (p0) REVERT: F 111 TYR cc_start: 0.5754 (OUTLIER) cc_final: 0.4810 (t80) REVERT: D 30 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6008 (pt0) REVERT: D 80 LYS cc_start: 0.7705 (tptt) cc_final: 0.7270 (tptt) REVERT: D 94 GLN cc_start: 0.5309 (OUTLIER) cc_final: 0.4942 (pt0) REVERT: G 108 ILE cc_start: 0.4494 (OUTLIER) cc_final: 0.3941 (pt) outliers start: 29 outliers final: 20 residues processed: 103 average time/residue: 0.0539 time to fit residues: 8.0758 Evaluate side-chains 104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 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 112 LEU Chi-restraints excluded: chain E residue 119 CYS 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 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 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 54 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN D 89 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.099396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.088398 restraints weight = 43822.325| |-----------------------------------------------------------------------------| r_work (start): 0.4144 rms_B_bonded: 6.66 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 6544 Z= 0.276 Angle : 0.958 19.349 8924 Z= 0.468 Chirality : 0.052 0.453 1056 Planarity : 0.006 0.055 1106 Dihedral : 9.446 58.011 1214 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.80 % Favored : 89.07 % Rotamer: Outliers : 5.94 % Allowed : 25.78 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.28), residues: 778 helix: -1.95 (0.42), residues: 110 sheet: -0.88 (0.36), residues: 185 loop : -1.98 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 117 TYR 0.026 0.003 TYR B 291 PHE 0.053 0.004 PHE A 263 TRP 0.035 0.003 TRP E 59 HIS 0.007 0.002 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00601 ( 6522) covalent geometry : angle 0.89503 ( 8871) SS BOND : bond 0.00802 ( 13) SS BOND : angle 1.64285 ( 26) hydrogen bonds : bond 0.04916 ( 184) hydrogen bonds : angle 7.60711 ( 462) link_BETA1-4 : bond 0.01035 ( 4) link_BETA1-4 : angle 3.46853 ( 12) link_NAG-ASN : bond 0.00630 ( 5) link_NAG-ASN : angle 7.64693 ( 15) *********************** 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: 38 poor density : 71 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9228 (tp30) cc_final: 0.9016 (tp30) REVERT: B 168 PHE cc_start: 0.4767 (OUTLIER) cc_final: 0.3269 (p90) REVERT: E 72 ASP cc_start: 0.7573 (t0) cc_final: 0.7288 (t0) REVERT: E 99 TYR cc_start: 0.4019 (OUTLIER) cc_final: 0.2667 (t80) REVERT: F 111 TYR cc_start: 0.6032 (OUTLIER) cc_final: 0.5142 (t80) REVERT: G 108 ILE cc_start: 0.5544 (OUTLIER) cc_final: 0.5009 (pt) outliers start: 38 outliers final: 28 residues processed: 100 average time/residue: 0.0708 time to fit residues: 9.9712 Evaluate side-chains 101 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 69 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN 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 54 TYR 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 191 ASP Chi-restraints excluded: chain B residue 206 TYR 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 89 GLU 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 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 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 68 ASP 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 27 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 65 optimal weight: 0.4980 chunk 68 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.102073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.091400 restraints weight = 41870.797| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 6.51 r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6544 Z= 0.159 Angle : 0.870 18.269 8924 Z= 0.416 Chirality : 0.049 0.451 1056 Planarity : 0.005 0.053 1106 Dihedral : 9.027 59.261 1214 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 19.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.58 % Favored : 92.29 % Rotamer: Outliers : 4.53 % Allowed : 28.12 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.29), residues: 778 helix: -1.50 (0.44), residues: 117 sheet: -0.79 (0.38), residues: 180 loop : -1.84 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 186 TYR 0.020 0.002 TYR B 291 PHE 0.052 0.003 PHE A 263 TRP 0.042 0.003 TRP E 59 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6522) covalent geometry : angle 0.81285 ( 8871) SS BOND : bond 0.00455 ( 13) SS BOND : angle 1.14345 ( 26) hydrogen bonds : bond 0.04033 ( 184) hydrogen bonds : angle 7.13069 ( 462) link_BETA1-4 : bond 0.01171 ( 4) link_BETA1-4 : angle 3.31905 ( 12) link_NAG-ASN : bond 0.00697 ( 5) link_NAG-ASN : angle 6.99869 ( 15) ********************** 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 104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9138 (tp30) cc_final: 0.8602 (tp30) REVERT: B 168 PHE cc_start: 0.4624 (OUTLIER) cc_final: 0.3294 (p90) REVERT: E 72 ASP cc_start: 0.7701 (t0) cc_final: 0.7373 (t0) REVERT: E 99 TYR cc_start: 0.3735 (OUTLIER) cc_final: 0.2476 (t80) REVERT: E 137 ASP cc_start: 0.8679 (OUTLIER) cc_final: 0.8316 (p0) REVERT: F 111 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.5011 (t80) REVERT: G 108 ILE cc_start: 0.4904 (OUTLIER) cc_final: 0.4191 (pt) outliers start: 29 outliers final: 22 residues processed: 99 average time/residue: 0.0708 time to fit residues: 9.9293 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 : 0.272 ------------------------------------------------------------------------------- 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 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 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 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 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 0.0670 chunk 18 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.101606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.091011 restraints weight = 42698.683| |-----------------------------------------------------------------------------| r_work (start): 0.4191 rms_B_bonded: 6.52 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6544 Z= 0.175 Angle : 0.866 17.499 8924 Z= 0.414 Chirality : 0.048 0.451 1056 Planarity : 0.005 0.051 1106 Dihedral : 9.005 58.726 1214 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.74 % Favored : 91.13 % Rotamer: Outliers : 4.53 % Allowed : 27.19 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.29), residues: 778 helix: -1.43 (0.45), residues: 117 sheet: -0.65 (0.38), residues: 176 loop : -1.84 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 117 TYR 0.021 0.002 TYR B 291 PHE 0.052 0.003 PHE A 263 TRP 0.037 0.002 TRP E 59 HIS 0.003 0.001 HIS B 155 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 6522) covalent geometry : angle 0.80937 ( 8871) SS BOND : bond 0.00516 ( 13) SS BOND : angle 1.36575 ( 26) hydrogen bonds : bond 0.04039 ( 184) hydrogen bonds : angle 7.12758 ( 462) link_BETA1-4 : bond 0.00979 ( 4) link_BETA1-4 : angle 3.27589 ( 12) link_NAG-ASN : bond 0.00688 ( 5) link_NAG-ASN : angle 6.84301 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1503.93 seconds wall clock time: 26 minutes 34.98 seconds (1594.98 seconds total)