Starting phenix.real_space_refine on Sat May 10 14:01:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw4_41658/05_2025/8tw4_41658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw4_41658/05_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_41658/05_2025/8tw4_41658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw4_41658/05_2025/8tw4_41658.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw4_41658/05_2025/8tw4_41658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw4_41658/05_2025/8tw4_41658.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 41 5.16 5 C 4076 2.51 5 N 1041 2.21 5 O 1243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6401 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1394 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 8, 'TRANS': 177} Chain breaks: 8 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1815 Classifications: {'peptide': 241} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 228} Chain breaks: 5 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 819 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 600 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 625 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 710 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "X" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 129 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 116 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.33, per 1000 atoms: 0.68 Number of scatterers: 6401 At special positions: 0 Unit cell: (95.04, 87.48, 110.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 41 16.00 O 1243 8.00 N 1041 7.00 C 4076 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 206 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 110 " distance=2.04 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 228 " distance=2.04 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.02 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03 Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03 Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.02 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.03 Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS Y 32 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " NAG-ASN " NAG A 302 " - " ASN A 41 " " NAG C 1 " - " ASN A 82 " " NAG G 201 " - " ASN G 92 " " NAG H 1 " - " ASN D 74 " " NAG I 1 " - " ASN G 52 " Time building additional restraints: 1.58 Conformation dependent library (CDL) restraints added in 796.2 milliseconds 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1554 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 16 sheets defined 20.2% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.968A pdb=" N ASN A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.543A pdb=" N MET A 188 " --> pdb=" O MET A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.851A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.528A pdb=" N PHE A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.833A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 157 removed outlier: 3.573A pdb=" N ILE B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.750A pdb=" N LEU B 285 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.579A pdb=" N MET B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 129 through 135 Processing helix chain 'E' and resid 135 through 144 Processing helix chain 'D' and resid 101 through 114 removed outlier: 4.001A pdb=" N GLY D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 128 through 129 No H-bonds generated for 'chain 'G' and resid 128 through 129' Processing helix chain 'X' and resid 32 through 36 Processing helix chain 'X' and resid 37 through 39 No H-bonds generated for 'chain 'X' and resid 37 through 39' Processing helix chain 'X' and resid 40 through 48 removed outlier: 3.606A pdb=" N ILE X 45 " --> pdb=" O ILE X 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 46 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.436A pdb=" N VAL A 32 " --> pdb=" O ILE A 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.682A pdb=" N LEU A 40 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 94 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68 removed outlier: 3.648A pdb=" N LEU A 67 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 108 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 144 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 65 removed outlier: 3.761A pdb=" N TRP B 53 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 142 through 145 removed outlier: 4.668A pdb=" N GLU B 142 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 182 through 183 removed outlier: 3.532A pdb=" N VAL B 230 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 37 through 41 removed outlier: 4.052A pdb=" N LYS E 37 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 39 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 83 " --> pdb=" O GLY E 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.915A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 94 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.573A pdb=" N LYS F 37 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 57 through 59 Processing sheet with id=AB4, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.673A pdb=" N TYR F 113 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE G 53 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE G 64 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TRP G 55 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.602A pdb=" N GLY G 75 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU G 44 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN G 73 " --> pdb=" O LEU G 44 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1992 1.34 - 1.46: 1459 1.46 - 1.58: 3017 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 6522 Sorted by residual: bond pdb=" N VAL E 118 " pdb=" CA VAL E 118 " ideal model delta sigma weight residual 1.452 1.495 -0.043 1.18e-02 7.18e+03 1.34e+01 bond pdb=" N CYS E 122 " pdb=" CA CYS E 122 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.17e-02 7.31e+03 8.55e+00 bond pdb=" N GLU E 120 " pdb=" CA GLU E 120 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.00e-02 1.00e+04 8.06e+00 bond pdb=" N CYS E 119 " pdb=" CA CYS E 119 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.61e+00 bond pdb=" N ASN E 121 " pdb=" CA ASN E 121 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.10e+00 ... (remaining 6517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 8786 3.50 - 7.01: 80 7.01 - 10.51: 4 10.51 - 14.02: 0 14.02 - 17.52: 1 Bond angle restraints: 8871 Sorted by residual: angle pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " pdb=" C5 NAG I 1 " ideal model delta sigma weight residual 113.21 130.73 -17.52 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C MET D 92 " pdb=" CA MET D 92 " pdb=" CB MET D 92 " ideal model delta sigma weight residual 116.54 110.14 6.40 1.15e+00 7.56e-01 3.10e+01 angle pdb=" C LYS G 51 " pdb=" N ASN G 52 " pdb=" CA ASN G 52 " ideal model delta sigma weight residual 121.89 130.81 -8.92 1.74e+00 3.30e-01 2.63e+01 angle pdb=" N CYS Y 32 " pdb=" CA CYS Y 32 " pdb=" C CYS Y 32 " ideal model delta sigma weight residual 114.31 109.06 5.25 1.29e+00 6.01e-01 1.66e+01 angle pdb=" C LEU D 29 " pdb=" N GLU D 30 " pdb=" CA GLU D 30 " ideal model delta sigma weight residual 121.54 128.52 -6.98 1.91e+00 2.74e-01 1.34e+01 ... (remaining 8866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 3542 16.87 - 33.74: 395 33.74 - 50.61: 118 50.61 - 67.48: 33 67.48 - 84.35: 12 Dihedral angle restraints: 4100 sinusoidal: 1706 harmonic: 2394 Sorted by residual: dihedral pdb=" CB CYS D 37 " pdb=" SG CYS D 37 " pdb=" SG CYS D 73 " pdb=" CB CYS D 73 " ideal model delta sinusoidal sigma weight residual -86.00 -161.22 75.22 1 1.00e+01 1.00e-02 7.15e+01 dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 122 " pdb=" CB CYS E 122 " ideal model delta sinusoidal sigma weight residual -86.00 -152.98 66.98 1 1.00e+01 1.00e-02 5.85e+01 dihedral pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " pdb=" SG CYS A 109 " pdb=" CB CYS A 109 " ideal model delta sinusoidal sigma weight residual 93.00 147.01 -54.01 1 1.00e+01 1.00e-02 3.96e+01 ... (remaining 4097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 989 0.090 - 0.181: 62 0.181 - 0.271: 3 0.271 - 0.362: 1 0.362 - 0.452: 1 Chirality restraints: 1056 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 5.72e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.12e+00 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.36 -0.04 2.00e-02 2.50e+03 3.74e+00 ... (remaining 1053 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 52 " 0.067 2.00e-02 2.50e+03 6.67e-02 5.55e+01 pdb=" CG ASN G 52 " -0.099 2.00e-02 2.50e+03 pdb=" OD1 ASN G 52 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN G 52 " -0.058 2.00e-02 2.50e+03 pdb=" C1 NAG I 1 " 0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 52 " 0.023 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" CG ASN G 52 " -0.083 2.00e-02 2.50e+03 pdb=" OD1 ASN G 52 " 0.032 2.00e-02 2.50e+03 pdb=" ND2 ASN G 52 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 74 " 0.029 2.00e-02 2.50e+03 2.74e-02 9.38e+00 pdb=" CG ASN D 74 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN D 74 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN D 74 " -0.029 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.029 2.00e-02 2.50e+03 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 160 2.66 - 3.22: 6236 3.22 - 3.78: 9795 3.78 - 4.34: 12830 4.34 - 4.90: 20352 Nonbonded interactions: 49373 Sorted by model distance: nonbonded pdb=" O ASP A 174 " pdb=" OG SER A 199 " model vdw 2.104 3.040 nonbonded pdb=" NH1 ARG E 117 " pdb=" O CYS D 96 " model vdw 2.132 3.120 nonbonded pdb=" OG SER B 254 " pdb=" OE2 GLU B 256 " model vdw 2.150 3.040 nonbonded pdb=" NE2 GLN B 25 " pdb=" O GLU B 125 " model vdw 2.203 3.120 nonbonded pdb=" O GLU A 36 " pdb=" OG SER A 99 " model vdw 2.228 3.040 ... (remaining 49368 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = (chain 'X' and (resid 32 or (resid 33 and (name N or name CA or name C or name O \ or name CB )) or resid 34 through 38 or (resid 39 and (name N or name CA or nam \ e C or name O or name CB )) or resid 40 through 43 or (resid 44 and (name N or n \ ame CA or name C or name O or name CB )) or resid 45 through 46)) selection = (chain 'Y' and (resid 32 through 34 or (resid 35 and (name N or name CA or name \ C or name O or name CB )) or resid 36 through 46)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 17.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.800 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.27), residues: 778 helix: -1.96 (0.42), residues: 115 sheet: -0.40 (0.37), residues: 184 loop : -1.87 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP E 59 HIS 0.003 0.001 HIS E 61 PHE 0.030 0.002 PHE G 118 TYR 0.019 0.002 TYR B 291 ARG 0.010 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.01116 ( 5) link_NAG-ASN : angle 6.97038 ( 15) link_BETA1-4 : bond 0.01466 ( 4) link_BETA1-4 : angle 4.56619 ( 12) hydrogen bonds : bond 0.25265 ( 184) hydrogen bonds : angle 10.14051 ( 462) SS BOND : bond 0.00532 ( 13) SS BOND : angle 1.37992 ( 26) covalent geometry : bond 0.00376 ( 6522) covalent geometry : angle 0.86194 ( 8871) *********************** 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 : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LYS cc_start: 0.6399 (ptpt) cc_final: 0.5903 (mmtm) REVERT: A 149 LYS cc_start: 0.9035 (tmtt) cc_final: 0.8637 (mmtt) REVERT: B 38 MET cc_start: 0.6639 (tpp) cc_final: 0.6116 (tpp) REVERT: B 168 PHE cc_start: 0.4745 (OUTLIER) cc_final: 0.3340 (p90) REVERT: B 252 ILE cc_start: 0.4803 (OUTLIER) cc_final: 0.4570 (tp) REVERT: E 89 GLU cc_start: 0.7600 (pt0) cc_final: 0.7307 (pt0) REVERT: E 125 MET cc_start: 0.5703 (pmm) cc_final: 0.5484 (pmm) REVERT: D 92 MET cc_start: 0.4834 (mmm) cc_final: 0.4476 (mmm) REVERT: G 108 ILE cc_start: 0.2528 (OUTLIER) cc_final: 0.1981 (pt) outliers start: 25 outliers final: 18 residues processed: 106 average time/residue: 0.1878 time to fit residues: 26.2768 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 : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 PHE Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 122 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain Y residue 40 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN E 61 HIS G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.108829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.098005 restraints weight = 40027.269| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 6.65 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6127 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6544 Z= 0.164 Angle : 0.836 12.815 8924 Z= 0.404 Chirality : 0.047 0.415 1056 Planarity : 0.005 0.053 1106 Dihedral : 10.052 56.928 1237 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 5.94 % Allowed : 20.16 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.28), residues: 778 helix: -1.57 (0.42), residues: 119 sheet: -0.20 (0.37), residues: 183 loop : -1.97 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 PHE 0.029 0.002 PHE G 118 TYR 0.022 0.002 TYR B 291 ARG 0.005 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 5) link_NAG-ASN : angle 6.01692 ( 15) link_BETA1-4 : bond 0.00906 ( 4) link_BETA1-4 : angle 3.46169 ( 12) hydrogen bonds : bond 0.04069 ( 184) hydrogen bonds : angle 7.65523 ( 462) SS BOND : bond 0.00401 ( 13) SS BOND : angle 0.97195 ( 26) covalent geometry : bond 0.00358 ( 6522) covalent geometry : angle 0.78876 ( 8871) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1556 Ramachandran restraints generated. 778 Oldfield, 0 Emsley, 778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8700 (tmtt) cc_final: 0.8484 (mmtt) REVERT: B 38 MET cc_start: 0.6653 (tpp) cc_final: 0.5930 (tpp) REVERT: B 155 HIS cc_start: 0.6818 (OUTLIER) cc_final: 0.6492 (p-80) REVERT: B 168 PHE cc_start: 0.4675 (OUTLIER) cc_final: 0.3322 (p90) REVERT: E 59 TRP cc_start: 0.6686 (m100) cc_final: 0.6451 (m100) REVERT: E 89 GLU cc_start: 0.7989 (pt0) cc_final: 0.7719 (pt0) REVERT: F 111 TYR cc_start: 0.5456 (OUTLIER) cc_final: 0.4153 (t80) REVERT: D 92 MET cc_start: 0.4288 (mmm) cc_final: 0.3939 (mmm) REVERT: D 94 GLN cc_start: 0.5252 (OUTLIER) cc_final: 0.4345 (pm20) outliers start: 38 outliers final: 19 residues processed: 107 average time/residue: 0.1607 time to fit residues: 23.5571 Evaluate side-chains 100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 27 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS F 61 HIS D 89 HIS G 73 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.101297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.090260 restraints weight = 42807.373| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 6.79 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 6544 Z= 0.305 Angle : 0.963 11.983 8924 Z= 0.484 Chirality : 0.051 0.446 1056 Planarity : 0.006 0.066 1106 Dihedral : 10.101 59.739 1218 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 26.10 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.00 % Favored : 90.87 % Rotamer: Outliers : 7.50 % Allowed : 20.00 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.28), residues: 778 helix: -2.18 (0.42), residues: 110 sheet: -0.64 (0.37), residues: 187 loop : -2.08 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 241 HIS 0.006 0.002 HIS B 225 PHE 0.046 0.004 PHE Y 40 TYR 0.030 0.003 TYR B 291 ARG 0.011 0.001 ARG F 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00798 ( 5) link_NAG-ASN : angle 6.06005 ( 15) link_BETA1-4 : bond 0.00787 ( 4) link_BETA1-4 : angle 3.34235 ( 12) hydrogen bonds : bond 0.05769 ( 184) hydrogen bonds : angle 8.18138 ( 462) SS BOND : bond 0.00862 ( 13) SS BOND : angle 1.57665 ( 26) covalent geometry : bond 0.00656 ( 6522) covalent geometry : angle 0.92129 ( 8871) *********************** 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 123 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 75 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9053 (OUTLIER) cc_final: 0.8577 (tp30) REVERT: B 155 HIS cc_start: 0.6843 (OUTLIER) cc_final: 0.6387 (p-80) REVERT: B 168 PHE cc_start: 0.5149 (OUTLIER) cc_final: 0.3269 (p90) REVERT: B 211 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7483 (mtm-85) REVERT: E 72 ASP cc_start: 0.8449 (t0) cc_final: 0.8243 (t0) REVERT: E 89 GLU cc_start: 0.7601 (pt0) cc_final: 0.7214 (pt0) REVERT: E 99 TYR cc_start: 0.4221 (OUTLIER) cc_final: 0.3580 (t80) REVERT: F 111 TYR cc_start: 0.5987 (OUTLIER) cc_final: 0.4825 (t80) REVERT: D 30 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6986 (pm20) REVERT: D 92 MET cc_start: 0.5526 (mmm) cc_final: 0.4990 (mmm) REVERT: D 94 GLN cc_start: 0.5304 (OUTLIER) cc_final: 0.5005 (pt0) outliers start: 48 outliers final: 29 residues processed: 115 average time/residue: 0.1765 time to fit residues: 27.6618 Evaluate side-chains 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 263 PHE 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 162 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 191 ASP Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 104 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 20 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 61 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.105781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.094869 restraints weight = 41912.685| |-----------------------------------------------------------------------------| r_work (start): 0.4249 rms_B_bonded: 6.88 r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6213 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6544 Z= 0.140 Angle : 0.856 23.135 8924 Z= 0.404 Chirality : 0.047 0.429 1056 Planarity : 0.004 0.049 1106 Dihedral : 9.528 56.002 1218 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.91 % Favored : 93.96 % Rotamer: Outliers : 4.84 % Allowed : 23.44 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.28), residues: 778 helix: -1.58 (0.44), residues: 116 sheet: -0.67 (0.38), residues: 172 loop : -1.91 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 241 HIS 0.003 0.001 HIS B 155 PHE 0.035 0.002 PHE B 93 TYR 0.018 0.002 TYR B 281 ARG 0.004 0.001 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00764 ( 5) link_NAG-ASN : angle 8.60901 ( 15) link_BETA1-4 : bond 0.01405 ( 4) link_BETA1-4 : angle 3.46282 ( 12) hydrogen bonds : bond 0.03802 ( 184) hydrogen bonds : angle 7.32317 ( 462) SS BOND : bond 0.00309 ( 13) SS BOND : angle 0.87075 ( 26) covalent geometry : bond 0.00307 ( 6522) covalent geometry : angle 0.77030 ( 8871) *********************** 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: 31 poor density : 84 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8966 (tp30) cc_final: 0.8542 (tp30) REVERT: A 149 LYS cc_start: 0.8715 (tmtt) cc_final: 0.8500 (mmtt) REVERT: A 157 LEU cc_start: 0.5213 (pp) cc_final: 0.4912 (pp) REVERT: B 38 MET cc_start: 0.7104 (tpp) cc_final: 0.6296 (tpp) REVERT: B 53 TRP cc_start: 0.6900 (m100) cc_final: 0.6556 (m100) REVERT: B 155 HIS cc_start: 0.6712 (OUTLIER) cc_final: 0.6462 (p-80) REVERT: B 168 PHE cc_start: 0.4489 (OUTLIER) cc_final: 0.3212 (p90) REVERT: E 72 ASP cc_start: 0.8096 (t0) cc_final: 0.7800 (t0) REVERT: E 89 GLU cc_start: 0.7942 (pt0) cc_final: 0.7658 (pt0) REVERT: E 99 TYR cc_start: 0.3818 (OUTLIER) cc_final: 0.3025 (t80) REVERT: E 125 MET cc_start: 0.6372 (pmm) cc_final: 0.6119 (pmm) REVERT: F 111 TYR cc_start: 0.5675 (OUTLIER) cc_final: 0.4494 (t80) REVERT: D 30 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6918 (pt0) REVERT: D 92 MET cc_start: 0.5345 (mmm) cc_final: 0.4581 (mmm) REVERT: G 108 ILE cc_start: 0.5046 (OUTLIER) cc_final: 0.4537 (pt) outliers start: 31 outliers final: 18 residues processed: 106 average time/residue: 0.1757 time to fit residues: 25.4182 Evaluate side-chains 100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 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 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 68 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 15 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 35 optimal weight: 0.0170 overall best weight: 1.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.103317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.092166 restraints weight = 42700.244| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 6.94 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.3005 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= 0.179 Angle : 0.837 18.132 8924 Z= 0.405 Chirality : 0.047 0.426 1056 Planarity : 0.005 0.053 1106 Dihedral : 9.424 57.879 1216 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.84 % Favored : 92.03 % Rotamer: Outliers : 5.62 % Allowed : 23.44 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.28), residues: 778 helix: -1.81 (0.42), residues: 117 sheet: -0.78 (0.38), residues: 179 loop : -1.89 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 55 HIS 0.003 0.001 HIS B 225 PHE 0.030 0.003 PHE B 93 TYR 0.024 0.002 TYR B 291 ARG 0.006 0.001 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00745 ( 5) link_NAG-ASN : angle 7.26035 ( 15) link_BETA1-4 : bond 0.01014 ( 4) link_BETA1-4 : angle 3.46241 ( 12) hydrogen bonds : bond 0.04075 ( 184) hydrogen bonds : angle 7.40146 ( 462) SS BOND : bond 0.00532 ( 13) SS BOND : angle 1.14536 ( 26) covalent geometry : bond 0.00393 ( 6522) covalent geometry : angle 0.77167 ( 8871) *********************** 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 112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8993 (tp30) cc_final: 0.8732 (tp30) REVERT: B 53 TRP cc_start: 0.7234 (m100) cc_final: 0.6968 (m100) REVERT: B 155 HIS cc_start: 0.6678 (OUTLIER) cc_final: 0.6423 (p-80) REVERT: B 168 PHE cc_start: 0.4802 (OUTLIER) cc_final: 0.3445 (p90) REVERT: E 55 SER cc_start: 0.8371 (OUTLIER) cc_final: 0.8150 (p) REVERT: E 59 TRP cc_start: 0.6769 (m100) cc_final: 0.6551 (m100) REVERT: E 72 ASP cc_start: 0.7944 (t0) cc_final: 0.7678 (t0) REVERT: E 89 GLU cc_start: 0.8101 (pt0) cc_final: 0.7634 (pt0) REVERT: E 99 TYR cc_start: 0.3936 (OUTLIER) cc_final: 0.2955 (t80) REVERT: E 117 ARG cc_start: 0.5685 (mmp-170) cc_final: 0.5096 (mmp80) REVERT: E 125 MET cc_start: 0.6258 (pmm) cc_final: 0.6016 (pmm) REVERT: F 111 TYR cc_start: 0.5820 (OUTLIER) cc_final: 0.4793 (t80) REVERT: D 30 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.7009 (pm20) REVERT: D 92 MET cc_start: 0.5372 (mmm) cc_final: 0.5158 (mmm) REVERT: D 94 GLN cc_start: 0.5458 (OUTLIER) cc_final: 0.5131 (pt0) REVERT: G 108 ILE cc_start: 0.4908 (OUTLIER) cc_final: 0.4329 (pt) outliers start: 36 outliers final: 23 residues processed: 106 average time/residue: 0.1361 time to fit residues: 20.5748 Evaluate side-chains 104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 73 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 SER 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 179 VAL Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 51 optimal weight: 0.4980 chunk 37 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 10 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN F 61 HIS ** 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 = 0.4370 r_free = 0.4370 target = 0.099336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.088453 restraints weight = 42804.143| |-----------------------------------------------------------------------------| r_work (start): 0.4141 rms_B_bonded: 6.71 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6544 Z= 0.232 Angle : 0.889 13.968 8924 Z= 0.440 Chirality : 0.049 0.462 1056 Planarity : 0.005 0.057 1106 Dihedral : 9.620 58.733 1214 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 24.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.28 % Favored : 89.59 % Rotamer: Outliers : 7.66 % Allowed : 22.97 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.28), residues: 778 helix: -2.04 (0.42), residues: 117 sheet: -1.31 (0.36), residues: 174 loop : -1.91 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 241 HIS 0.004 0.001 HIS B 185 PHE 0.033 0.003 PHE B 93 TYR 0.026 0.002 TYR B 291 ARG 0.008 0.001 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00608 ( 5) link_NAG-ASN : angle 6.41060 ( 15) link_BETA1-4 : bond 0.00848 ( 4) link_BETA1-4 : angle 3.46357 ( 12) hydrogen bonds : bond 0.04874 ( 184) hydrogen bonds : angle 7.69409 ( 462) SS BOND : bond 0.00685 ( 13) SS BOND : angle 1.46629 ( 26) covalent geometry : bond 0.00504 ( 6522) covalent geometry : angle 0.83890 ( 8871) *********************** 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 121 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 72 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9123 (tp30) cc_final: 0.8796 (tp30) REVERT: B 132 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6509 (mt) REVERT: B 155 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.6180 (p-80) REVERT: B 168 PHE cc_start: 0.5090 (OUTLIER) cc_final: 0.3639 (p90) REVERT: E 55 SER cc_start: 0.8299 (OUTLIER) cc_final: 0.8016 (p) REVERT: E 89 GLU cc_start: 0.7902 (pt0) cc_final: 0.7587 (pt0) REVERT: E 99 TYR cc_start: 0.4049 (OUTLIER) cc_final: 0.2819 (t80) REVERT: E 117 ARG cc_start: 0.5867 (mmp-170) cc_final: 0.5552 (mmp-170) REVERT: F 111 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.5182 (t80) REVERT: D 30 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.7134 (pm20) REVERT: D 92 MET cc_start: 0.5541 (mmm) cc_final: 0.5169 (mmp) REVERT: D 94 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.5332 (pt0) REVERT: G 108 ILE cc_start: 0.5198 (OUTLIER) cc_final: 0.4637 (pt) outliers start: 49 outliers final: 31 residues processed: 116 average time/residue: 0.1520 time to fit residues: 24.5899 Evaluate side-chains 108 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 68 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 SER 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 132 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 190 THR 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 55 SER Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 52 ASN Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 115 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.7980 chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN F 61 HIS ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.101753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.090997 restraints weight = 42240.596| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 6.73 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6339 moved from start: 0.4015 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= 0.140 Angle : 0.800 13.795 8924 Z= 0.385 Chirality : 0.047 0.445 1056 Planarity : 0.004 0.051 1106 Dihedral : 9.206 58.736 1214 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.20 % Favored : 92.67 % Rotamer: Outliers : 6.09 % Allowed : 25.78 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.29), residues: 778 helix: -1.59 (0.44), residues: 117 sheet: -1.11 (0.37), residues: 168 loop : -1.79 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 PHE 0.028 0.002 PHE Y 40 TYR 0.020 0.002 TYR B 291 ARG 0.004 0.001 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00697 ( 5) link_NAG-ASN : angle 6.12717 ( 15) link_BETA1-4 : bond 0.00857 ( 4) link_BETA1-4 : angle 3.26468 ( 12) hydrogen bonds : bond 0.03674 ( 184) hydrogen bonds : angle 7.20137 ( 462) SS BOND : bond 0.00420 ( 13) SS BOND : angle 1.08297 ( 26) covalent geometry : bond 0.00310 ( 6522) covalent geometry : angle 0.75030 ( 8871) *********************** 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 115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 76 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9098 (tp30) cc_final: 0.8545 (tp30) REVERT: B 132 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6552 (mt) REVERT: B 168 PHE cc_start: 0.4772 (OUTLIER) cc_final: 0.3293 (p90) REVERT: E 55 SER cc_start: 0.8155 (OUTLIER) cc_final: 0.7882 (p) REVERT: E 59 TRP cc_start: 0.6710 (m100) cc_final: 0.6463 (m100) REVERT: E 72 ASP cc_start: 0.7369 (t0) cc_final: 0.7107 (t0) REVERT: E 89 GLU cc_start: 0.8051 (pt0) cc_final: 0.7685 (pt0) REVERT: E 99 TYR cc_start: 0.3840 (OUTLIER) cc_final: 0.2743 (t80) REVERT: E 117 ARG cc_start: 0.5711 (mmp-170) cc_final: 0.5475 (mmp-170) REVERT: E 137 ASP cc_start: 0.8654 (OUTLIER) cc_final: 0.8438 (p0) REVERT: F 111 TYR cc_start: 0.5922 (OUTLIER) cc_final: 0.4947 (t80) REVERT: D 30 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7182 (pm20) REVERT: D 92 MET cc_start: 0.5347 (mmm) cc_final: 0.4955 (mmm) REVERT: G 108 ILE cc_start: 0.5050 (OUTLIER) cc_final: 0.4398 (pt) outliers start: 39 outliers final: 25 residues processed: 109 average time/residue: 0.1356 time to fit residues: 21.3717 Evaluate side-chains 104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 71 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 52 ASN 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 22 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.100311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.089437 restraints weight = 43444.874| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 6.66 r_work (final): 0.4151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6544 Z= 0.193 Angle : 0.843 12.930 8924 Z= 0.411 Chirality : 0.048 0.449 1056 Planarity : 0.005 0.055 1106 Dihedral : 9.269 56.407 1214 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.90 % Favored : 89.97 % Rotamer: Outliers : 6.88 % Allowed : 25.31 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.38 (0.29), residues: 778 helix: -1.78 (0.43), residues: 117 sheet: -1.25 (0.37), residues: 177 loop : -1.69 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 241 HIS 0.007 0.001 HIS B 155 PHE 0.024 0.003 PHE G 120 TYR 0.024 0.002 TYR B 291 ARG 0.004 0.001 ARG F 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00648 ( 5) link_NAG-ASN : angle 6.07611 ( 15) link_BETA1-4 : bond 0.00843 ( 4) link_BETA1-4 : angle 3.23876 ( 12) hydrogen bonds : bond 0.04326 ( 184) hydrogen bonds : angle 7.36850 ( 462) SS BOND : bond 0.00563 ( 13) SS BOND : angle 1.26862 ( 26) covalent geometry : bond 0.00426 ( 6522) covalent geometry : angle 0.79595 ( 8871) *********************** 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 117 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 73 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9163 (OUTLIER) cc_final: 0.8647 (tp30) REVERT: B 132 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6488 (mt) REVERT: B 168 PHE cc_start: 0.4951 (OUTLIER) cc_final: 0.3369 (p90) REVERT: E 55 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8021 (p) REVERT: E 59 TRP cc_start: 0.6695 (m100) cc_final: 0.6436 (m100) REVERT: E 72 ASP cc_start: 0.7521 (t0) cc_final: 0.7269 (t0) REVERT: E 81 HIS cc_start: 0.7878 (m-70) cc_final: 0.7519 (m-70) REVERT: E 89 GLU cc_start: 0.7981 (pt0) cc_final: 0.7642 (pt0) REVERT: E 99 TYR cc_start: 0.3882 (OUTLIER) cc_final: 0.2633 (t80) REVERT: F 111 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5073 (t80) REVERT: D 30 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6830 (pm20) REVERT: D 92 MET cc_start: 0.5661 (mmm) cc_final: 0.5091 (ptt) REVERT: G 108 ILE cc_start: 0.5300 (OUTLIER) cc_final: 0.4654 (pt) outliers start: 44 outliers final: 31 residues processed: 111 average time/residue: 0.1374 time to fit residues: 21.8985 Evaluate side-chains 110 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 71 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 111 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 52 ASN 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 G residue 115 ILE Chi-restraints excluded: chain X residue 44 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 43 optimal weight: 0.0170 chunk 31 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 7 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.103388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.092946 restraints weight = 42301.799| |-----------------------------------------------------------------------------| r_work (start): 0.4224 rms_B_bonded: 6.46 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.4356 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= 0.131 Angle : 0.802 12.515 8924 Z= 0.386 Chirality : 0.046 0.433 1056 Planarity : 0.004 0.050 1106 Dihedral : 8.921 55.806 1214 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.30 % Favored : 93.57 % Rotamer: Outliers : 5.62 % Allowed : 26.56 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.30), residues: 778 helix: -1.37 (0.45), residues: 117 sheet: -0.99 (0.37), residues: 184 loop : -1.69 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 PHE 0.026 0.002 PHE Y 40 TYR 0.013 0.001 TYR B 291 ARG 0.004 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00757 ( 5) link_NAG-ASN : angle 5.70883 ( 15) link_BETA1-4 : bond 0.00856 ( 4) link_BETA1-4 : angle 3.08960 ( 12) hydrogen bonds : bond 0.03584 ( 184) hydrogen bonds : angle 6.89607 ( 462) SS BOND : bond 0.00306 ( 13) SS BOND : angle 0.91374 ( 26) covalent geometry : bond 0.00290 ( 6522) covalent geometry : angle 0.75886 ( 8871) *********************** 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 115 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9036 (tp30) cc_final: 0.8477 (tp30) REVERT: A 149 LYS cc_start: 0.8740 (tmtt) cc_final: 0.8500 (mmtt) REVERT: A 157 LEU cc_start: 0.5306 (pp) cc_final: 0.5010 (pp) REVERT: B 53 TRP cc_start: 0.7031 (m100) cc_final: 0.6725 (m100) REVERT: B 132 LEU cc_start: 0.6971 (OUTLIER) cc_final: 0.6654 (mt) REVERT: B 168 PHE cc_start: 0.4477 (OUTLIER) cc_final: 0.3193 (p90) REVERT: E 55 SER cc_start: 0.8156 (OUTLIER) cc_final: 0.7888 (p) REVERT: E 59 TRP cc_start: 0.6568 (m100) cc_final: 0.6307 (m100) REVERT: E 72 ASP cc_start: 0.7394 (t0) cc_final: 0.7117 (t0) REVERT: E 81 HIS cc_start: 0.7745 (m-70) cc_final: 0.7386 (m-70) REVERT: E 89 GLU cc_start: 0.8081 (pt0) cc_final: 0.7635 (pt0) REVERT: E 99 TYR cc_start: 0.3566 (OUTLIER) cc_final: 0.2393 (t80) REVERT: E 123 MET cc_start: 0.6647 (pmm) cc_final: 0.6140 (pmm) REVERT: F 111 TYR cc_start: 0.5738 (OUTLIER) cc_final: 0.4877 (t80) REVERT: G 86 GLN cc_start: 0.2477 (OUTLIER) cc_final: 0.2194 (pm20) REVERT: G 108 ILE cc_start: 0.4911 (OUTLIER) cc_final: 0.4256 (pt) outliers start: 36 outliers final: 24 residues processed: 108 average time/residue: 0.1387 time to fit residues: 21.5221 Evaluate side-chains 106 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 75 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 249 SER 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 132 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 55 SER 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 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 52 ASN Chi-restraints excluded: chain G residue 76 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 121 ASN G 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.101536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.090832 restraints weight = 43809.343| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 6.70 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6544 Z= 0.165 Angle : 0.826 11.996 8924 Z= 0.401 Chirality : 0.047 0.433 1056 Planarity : 0.005 0.052 1106 Dihedral : 8.892 58.853 1212 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.61 % Favored : 91.26 % Rotamer: Outliers : 5.62 % Allowed : 27.34 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.30), residues: 778 helix: -1.28 (0.46), residues: 116 sheet: -1.12 (0.38), residues: 181 loop : -1.63 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 177 HIS 0.004 0.001 HIS B 155 PHE 0.029 0.002 PHE B 93 TYR 0.021 0.002 TYR B 291 ARG 0.008 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 5) link_NAG-ASN : angle 5.73640 ( 15) link_BETA1-4 : bond 0.00803 ( 4) link_BETA1-4 : angle 3.03001 ( 12) hydrogen bonds : bond 0.03786 ( 184) hydrogen bonds : angle 6.95725 ( 462) SS BOND : bond 0.00514 ( 13) SS BOND : angle 1.14829 ( 26) covalent geometry : bond 0.00367 ( 6522) covalent geometry : angle 0.78383 ( 8871) ********************** 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 112 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 76 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9065 (tp30) cc_final: 0.8614 (tp30) REVERT: A 149 LYS cc_start: 0.8664 (tmtt) cc_final: 0.8411 (mmtt) REVERT: A 157 LEU cc_start: 0.5444 (pp) cc_final: 0.5113 (pp) REVERT: B 53 TRP cc_start: 0.7278 (m100) cc_final: 0.7026 (m100) REVERT: B 132 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6590 (mt) REVERT: B 168 PHE cc_start: 0.4513 (OUTLIER) cc_final: 0.3174 (p90) REVERT: E 59 TRP cc_start: 0.6588 (m100) cc_final: 0.6347 (m100) REVERT: E 72 ASP cc_start: 0.7376 (t0) cc_final: 0.7114 (t0) REVERT: E 81 HIS cc_start: 0.7841 (m-70) cc_final: 0.7486 (m-70) REVERT: E 89 GLU cc_start: 0.7901 (pt0) cc_final: 0.7598 (pt0) REVERT: E 99 TYR cc_start: 0.3683 (OUTLIER) cc_final: 0.2366 (t80) REVERT: F 111 TYR cc_start: 0.5800 (OUTLIER) cc_final: 0.5014 (t80) REVERT: G 86 GLN cc_start: 0.3142 (OUTLIER) cc_final: 0.2513 (pm20) REVERT: G 93 LYS cc_start: -0.1185 (OUTLIER) cc_final: -0.1417 (mttp) REVERT: G 108 ILE cc_start: 0.4920 (OUTLIER) cc_final: 0.4260 (pt) REVERT: X 45 ILE cc_start: 0.8772 (mm) cc_final: 0.8551 (tp) outliers start: 36 outliers final: 25 residues processed: 105 average time/residue: 0.1444 time to fit residues: 21.5527 Evaluate side-chains 107 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 75 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 MET Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 249 SER Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain 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 52 ASN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 86 GLN Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 38 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 76 optimal weight: 0.0770 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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 = 0.4418 r_free = 0.4418 target = 0.102213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.091470 restraints weight = 43920.684| |-----------------------------------------------------------------------------| r_work (start): 0.4200 rms_B_bonded: 6.77 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6544 Z= 0.143 Angle : 0.813 11.872 8924 Z= 0.393 Chirality : 0.046 0.433 1056 Planarity : 0.005 0.050 1106 Dihedral : 8.843 59.532 1212 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.84 % Favored : 92.03 % Rotamer: Outliers : 5.31 % Allowed : 27.81 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.30), residues: 778 helix: -1.25 (0.46), residues: 116 sheet: -1.02 (0.40), residues: 169 loop : -1.54 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 55 HIS 0.003 0.001 HIS B 155 PHE 0.026 0.002 PHE B 93 TYR 0.019 0.001 TYR B 291 ARG 0.007 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00699 ( 5) link_NAG-ASN : angle 5.62039 ( 15) link_BETA1-4 : bond 0.00777 ( 4) link_BETA1-4 : angle 2.99169 ( 12) hydrogen bonds : bond 0.03541 ( 184) hydrogen bonds : angle 6.82941 ( 462) SS BOND : bond 0.00411 ( 13) SS BOND : angle 1.12740 ( 26) covalent geometry : bond 0.00320 ( 6522) covalent geometry : angle 0.77188 ( 8871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3211.10 seconds wall clock time: 56 minutes 38.39 seconds (3398.39 seconds total)