Starting phenix.real_space_refine on Sun Apr 27 18:49:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tw4_41658/04_2025/8tw4_41658.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tw4_41658/04_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_41658/04_2025/8tw4_41658.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tw4_41658/04_2025/8tw4_41658.map" model { file = "/net/cci-nas-00/data/ceres_data/8tw4_41658/04_2025/8tw4_41658.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tw4_41658/04_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-5669/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: 4.15, per 1000 atoms: 0.65 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: 1.70 Conformation dependent library (CDL) restraints added in 841.9 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: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 162 through 166 removed outlier: 3.968A pdb=" N ASN A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.543A pdb=" N MET A 188 " --> pdb=" O MET A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.851A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.528A pdb=" N PHE A 253 " --> pdb=" O SER A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 3.833A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 157 removed outlier: 3.573A pdb=" N ILE B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 287 removed outlier: 3.750A pdb=" N LEU B 285 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.579A pdb=" N MET B 303 " --> pdb=" O VAL B 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 128 No H-bonds generated for 'chain 'E' and resid 126 through 128' Processing helix chain 'E' and resid 129 through 135 Processing helix chain 'E' and resid 135 through 144 Processing helix chain 'D' and resid 101 through 114 removed outlier: 4.001A pdb=" N GLY D 106 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE D 107 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP D 111 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 128 through 129 No H-bonds generated for 'chain 'G' and resid 128 through 129' Processing helix chain 'X' and resid 32 through 36 Processing helix chain 'X' and resid 37 through 39 No H-bonds generated for 'chain 'X' and resid 37 through 39' Processing helix chain 'X' and resid 40 through 48 removed outlier: 3.606A pdb=" N ILE X 45 " --> pdb=" O ILE X 41 " (cutoff:3.500A) Processing helix chain 'Y' and resid 32 through 46 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 removed outlier: 4.436A pdb=" N VAL A 32 " --> pdb=" O ILE A 130 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.682A pdb=" N LEU A 40 " --> pdb=" O LEU A 94 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N LEU A 94 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 67 through 68 removed outlier: 3.648A pdb=" N LEU A 67 " --> pdb=" O TRP A 54 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU A 108 " --> pdb=" O PHE A 55 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 144 Processing sheet with id=AA5, first strand: chain 'B' and resid 24 through 26 Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 65 removed outlier: 3.761A pdb=" N TRP B 53 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 142 through 145 removed outlier: 4.668A pdb=" N GLU B 142 " --> pdb=" O THR B 166 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 182 through 183 removed outlier: 3.532A pdb=" N VAL B 230 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 37 through 41 removed outlier: 4.052A pdb=" N LYS E 37 " --> pdb=" O THR E 48 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 39 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER E 83 " --> pdb=" O GLY E 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.915A pdb=" N TRP E 59 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 94 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 37 through 38 removed outlier: 3.573A pdb=" N LYS F 37 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 57 through 59 Processing sheet with id=AB4, first strand: chain 'F' and resid 95 through 96 removed outlier: 6.673A pdb=" N TYR F 113 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE G 53 " --> pdb=" O PHE G 64 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N PHE G 64 " --> pdb=" O ILE G 53 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TRP G 55 " --> pdb=" O ILE G 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 42 through 43 Processing sheet with id=AB6, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB7, first strand: chain 'G' and resid 31 through 32 removed outlier: 3.602A pdb=" N GLY G 75 " --> pdb=" O VAL G 42 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N LEU G 44 " --> pdb=" O ASN G 73 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN G 73 " --> pdb=" O LEU G 44 " (cutoff:3.500A) 184 hydrogen bonds defined for protein. 462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.56 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: 1.110 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: 0.060 Process input model: 18.060 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.320 ------------------------------------------------------------------------------- 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 : 0.741 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: 0.1904 time to fit residues: 26.6340 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 : 0.730 ------------------------------------------------------------------------------- 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: 0.9990 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: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 61 HIS G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.108815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.098000 restraints weight = 40133.263| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 6.64 r_work (final): 0.4285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6129 moved from start: 0.1289 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= 0.163 Angle : 0.836 12.811 8924 Z= 0.404 Chirality : 0.047 0.414 1056 Planarity : 0.005 0.053 1106 Dihedral : 10.048 56.962 1237 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 16.45 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: -1.56 (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 0.019 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 PHE 0.030 0.002 PHE G 118 TYR 0.022 0.002 TYR B 291 ARG 0.007 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 5) link_NAG-ASN : angle 6.00130 ( 15) link_BETA1-4 : bond 0.00928 ( 4) link_BETA1-4 : angle 3.43967 ( 12) hydrogen bonds : bond 0.04024 ( 184) hydrogen bonds : angle 7.63994 ( 462) SS BOND : bond 0.00407 ( 13) SS BOND : angle 0.96861 ( 26) covalent geometry : bond 0.00358 ( 6522) covalent geometry : angle 0.78969 ( 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 : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 LYS cc_start: 0.8721 (tmtt) cc_final: 0.8493 (mmtt) REVERT: B 38 MET cc_start: 0.6669 (tpp) cc_final: 0.5940 (tpp) REVERT: B 155 HIS cc_start: 0.6769 (OUTLIER) cc_final: 0.6436 (p-80) REVERT: B 168 PHE cc_start: 0.4671 (OUTLIER) cc_final: 0.3322 (p90) REVERT: E 59 TRP cc_start: 0.6684 (m100) cc_final: 0.6450 (m100) REVERT: E 89 GLU cc_start: 0.7996 (pt0) cc_final: 0.7724 (pt0) REVERT: F 111 TYR cc_start: 0.5453 (OUTLIER) cc_final: 0.4149 (t80) REVERT: D 92 MET cc_start: 0.4280 (mmm) cc_final: 0.3934 (mmm) REVERT: D 94 GLN cc_start: 0.5268 (OUTLIER) cc_final: 0.4356 (pm20) outliers start: 38 outliers final: 19 residues processed: 107 average time/residue: 0.1743 time to fit residues: 25.5523 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 : 0.726 ------------------------------------------------------------------------------- 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: 2.9990 chunk 68 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 HIS B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.105702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.094546 restraints weight = 41889.762| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 6.94 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 6544 Z= 0.193 Angle : 0.822 12.388 8924 Z= 0.405 Chirality : 0.047 0.421 1056 Planarity : 0.005 0.055 1106 Dihedral : 9.460 58.946 1218 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.71 % Favored : 92.16 % Rotamer: Outliers : 5.94 % Allowed : 21.09 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.28), residues: 778 helix: -1.66 (0.43), residues: 116 sheet: -0.34 (0.37), residues: 176 loop : -1.95 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 241 HIS 0.004 0.001 HIS B 225 PHE 0.041 0.002 PHE Y 40 TYR 0.024 0.002 TYR B 291 ARG 0.009 0.001 ARG E 101 Details of bonding type rmsd link_NAG-ASN : bond 0.00796 ( 5) link_NAG-ASN : angle 5.88682 ( 15) link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 3.03259 ( 12) hydrogen bonds : bond 0.04370 ( 184) hydrogen bonds : angle 7.52509 ( 462) SS BOND : bond 0.00517 ( 13) SS BOND : angle 1.04554 ( 26) covalent geometry : bond 0.00423 ( 6522) covalent geometry : angle 0.77828 ( 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 116 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 78 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8932 (tp30) cc_final: 0.8436 (tp30) REVERT: A 87 LYS cc_start: 0.7022 (ptpt) cc_final: 0.6333 (tptt) REVERT: B 38 MET cc_start: 0.6988 (tpp) cc_final: 0.6317 (tpp) REVERT: B 155 HIS cc_start: 0.6774 (OUTLIER) cc_final: 0.6465 (p-80) REVERT: B 168 PHE cc_start: 0.4757 (OUTLIER) cc_final: 0.3290 (p90) REVERT: E 72 ASP cc_start: 0.8340 (t0) cc_final: 0.8091 (t0) REVERT: E 89 GLU cc_start: 0.7805 (pt0) cc_final: 0.7596 (pt0) REVERT: E 99 TYR cc_start: 0.3877 (OUTLIER) cc_final: 0.3201 (t80) REVERT: F 111 TYR cc_start: 0.5757 (OUTLIER) cc_final: 0.4570 (t80) REVERT: D 30 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6678 (pt0) REVERT: D 92 MET cc_start: 0.5013 (mmm) cc_final: 0.4571 (mmm) REVERT: D 94 GLN cc_start: 0.5130 (OUTLIER) cc_final: 0.4780 (pt0) outliers start: 38 outliers final: 22 residues processed: 109 average time/residue: 0.1834 time to fit residues: 27.3825 Evaluate side-chains 99 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 211 ARG Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 40 ILE Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 76 SER 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: 0.2980 chunk 38 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.106777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.095776 restraints weight = 41892.223| |-----------------------------------------------------------------------------| r_work (start): 0.4247 rms_B_bonded: 6.94 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6544 Z= 0.140 Angle : 0.775 11.815 8924 Z= 0.376 Chirality : 0.046 0.418 1056 Planarity : 0.004 0.048 1106 Dihedral : 9.157 55.937 1216 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.56 % Favored : 93.32 % Rotamer: Outliers : 4.84 % Allowed : 22.97 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.28), residues: 778 helix: -1.48 (0.44), residues: 116 sheet: -0.34 (0.39), residues: 169 loop : -1.88 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 59 HIS 0.003 0.001 HIS B 225 PHE 0.032 0.002 PHE G 120 TYR 0.020 0.002 TYR B 291 ARG 0.004 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00890 ( 5) link_NAG-ASN : angle 5.66446 ( 15) link_BETA1-4 : bond 0.00575 ( 4) link_BETA1-4 : angle 2.99697 ( 12) hydrogen bonds : bond 0.03798 ( 184) hydrogen bonds : angle 7.16038 ( 462) SS BOND : bond 0.00364 ( 13) SS BOND : angle 0.87335 ( 26) covalent geometry : bond 0.00306 ( 6522) covalent geometry : angle 0.73187 ( 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 111 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8958 (tp30) cc_final: 0.8693 (tp30) REVERT: A 186 ARG cc_start: 0.6904 (ttt180) cc_final: 0.6650 (ttt90) REVERT: B 155 HIS cc_start: 0.6665 (OUTLIER) cc_final: 0.6412 (p-80) REVERT: B 168 PHE cc_start: 0.4621 (OUTLIER) cc_final: 0.3340 (p90) REVERT: E 72 ASP cc_start: 0.7930 (t0) cc_final: 0.7609 (t0) REVERT: E 89 GLU cc_start: 0.7863 (pt0) cc_final: 0.7587 (pt0) REVERT: E 99 TYR cc_start: 0.4174 (OUTLIER) cc_final: 0.3096 (t80) REVERT: E 125 MET cc_start: 0.6272 (pmm) cc_final: 0.5984 (pmm) REVERT: F 111 TYR cc_start: 0.5647 (OUTLIER) cc_final: 0.4555 (t80) REVERT: D 92 MET cc_start: 0.5184 (mmm) cc_final: 0.4666 (mmt) REVERT: G 108 ILE cc_start: 0.4957 (OUTLIER) cc_final: 0.4372 (pt) outliers start: 31 outliers final: 21 residues processed: 105 average time/residue: 0.1612 time to fit residues: 23.4605 Evaluate side-chains 99 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 73 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 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: 0.7980 chunk 66 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 0.0870 chunk 25 optimal weight: 0.0870 chunk 35 optimal weight: 0.2980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.108466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.097535 restraints weight = 41742.867| |-----------------------------------------------------------------------------| r_work (start): 0.4286 rms_B_bonded: 6.92 r_work (final): 0.4286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6544 Z= 0.115 Angle : 0.735 11.182 8924 Z= 0.356 Chirality : 0.045 0.403 1056 Planarity : 0.004 0.047 1106 Dihedral : 8.808 58.360 1216 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.04 % Favored : 93.83 % Rotamer: Outliers : 3.91 % Allowed : 24.22 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.08 (0.29), residues: 778 helix: -1.51 (0.43), residues: 121 sheet: -0.43 (0.39), residues: 166 loop : -1.76 (0.27), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 55 HIS 0.002 0.001 HIS B 225 PHE 0.041 0.002 PHE A 263 TYR 0.014 0.001 TYR B 281 ARG 0.002 0.000 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00908 ( 5) link_NAG-ASN : angle 5.43953 ( 15) link_BETA1-4 : bond 0.00537 ( 4) link_BETA1-4 : angle 2.88221 ( 12) hydrogen bonds : bond 0.03449 ( 184) hydrogen bonds : angle 6.72042 ( 462) SS BOND : bond 0.00262 ( 13) SS BOND : angle 0.74810 ( 26) covalent geometry : bond 0.00247 ( 6522) covalent geometry : angle 0.69370 ( 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 107 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8851 (tp30) cc_final: 0.8562 (tp30) REVERT: B 109 PHE cc_start: 0.8412 (m-80) cc_final: 0.8187 (m-10) REVERT: B 168 PHE cc_start: 0.4216 (OUTLIER) cc_final: 0.3076 (p90) REVERT: E 72 ASP cc_start: 0.7867 (t0) cc_final: 0.7494 (t0) REVERT: E 89 GLU cc_start: 0.8127 (pt0) cc_final: 0.7813 (pt0) REVERT: E 99 TYR cc_start: 0.3742 (OUTLIER) cc_final: 0.2748 (t80) REVERT: E 123 MET cc_start: 0.6721 (pmm) cc_final: 0.6233 (pmm) REVERT: E 125 MET cc_start: 0.5977 (pmm) cc_final: 0.5741 (pmm) REVERT: E 137 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.8068 (p0) REVERT: F 111 TYR cc_start: 0.5524 (OUTLIER) cc_final: 0.4482 (t80) REVERT: D 80 LYS cc_start: 0.7452 (tptt) cc_final: 0.7160 (tptt) outliers start: 25 outliers final: 15 residues processed: 100 average time/residue: 0.1764 time to fit residues: 24.0714 Evaluate side-chains 95 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 104 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 35 optimal weight: 0.1980 chunk 54 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 5 optimal weight: 0.0470 overall best weight: 1.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 HIS ** 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 = 0.4473 r_free = 0.4473 target = 0.106549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.095630 restraints weight = 41936.801| |-----------------------------------------------------------------------------| r_work (start): 0.4251 rms_B_bonded: 6.88 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.2842 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= 0.137 Angle : 0.749 10.961 8924 Z= 0.364 Chirality : 0.045 0.402 1056 Planarity : 0.004 0.046 1106 Dihedral : 8.739 59.215 1216 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.68 % Favored : 93.19 % Rotamer: Outliers : 4.53 % Allowed : 25.16 % Favored : 70.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.07 (0.29), residues: 778 helix: -1.59 (0.42), residues: 121 sheet: -0.33 (0.38), residues: 177 loop : -1.80 (0.28), residues: 480 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 0.045 0.003 PHE A 263 TYR 0.019 0.001 TYR B 291 ARG 0.007 0.001 ARG D 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00826 ( 5) link_NAG-ASN : angle 5.36849 ( 15) link_BETA1-4 : bond 0.00442 ( 4) link_BETA1-4 : angle 2.87206 ( 12) hydrogen bonds : bond 0.03752 ( 184) hydrogen bonds : angle 6.74457 ( 462) SS BOND : bond 0.00378 ( 13) SS BOND : angle 0.89103 ( 26) covalent geometry : bond 0.00298 ( 6522) covalent geometry : angle 0.70884 ( 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 106 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8971 (tp30) cc_final: 0.8701 (tp30) REVERT: A 149 LYS cc_start: 0.8604 (tmtt) cc_final: 0.8312 (mmtt) REVERT: A 157 LEU cc_start: 0.5332 (tp) cc_final: 0.5009 (tp) REVERT: B 46 MET cc_start: 0.7079 (mtt) cc_final: 0.6785 (mpp) REVERT: B 168 PHE cc_start: 0.4667 (OUTLIER) cc_final: 0.3413 (p90) REVERT: E 59 TRP cc_start: 0.6179 (m100) cc_final: 0.5956 (m100) REVERT: E 72 ASP cc_start: 0.7755 (t0) cc_final: 0.7437 (t0) REVERT: E 89 GLU cc_start: 0.8060 (pt0) cc_final: 0.7833 (pt0) REVERT: E 99 TYR cc_start: 0.3967 (OUTLIER) cc_final: 0.2775 (t80) REVERT: F 111 TYR cc_start: 0.5594 (OUTLIER) cc_final: 0.4608 (t80) REVERT: D 30 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6195 (pt0) REVERT: D 94 GLN cc_start: 0.5379 (OUTLIER) cc_final: 0.5020 (pt0) REVERT: G 84 MET cc_start: 0.4176 (tmm) cc_final: 0.3880 (tmm) REVERT: G 108 ILE cc_start: 0.4761 (OUTLIER) cc_final: 0.4203 (pt) outliers start: 29 outliers final: 21 residues processed: 100 average time/residue: 0.1451 time to fit residues: 21.1216 Evaluate side-chains 100 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 67 TYR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 168 PHE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 67 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.106696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.095745 restraints weight = 41052.779| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 6.87 r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6150 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6544 Z= 0.120 Angle : 0.738 10.753 8924 Z= 0.354 Chirality : 0.045 0.401 1056 Planarity : 0.004 0.045 1106 Dihedral : 8.601 59.584 1214 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.43 % Favored : 93.44 % Rotamer: Outliers : 4.38 % Allowed : 26.09 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.29), residues: 778 helix: -1.40 (0.43), residues: 121 sheet: -0.34 (0.39), residues: 171 loop : -1.73 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 55 HIS 0.003 0.001 HIS B 155 PHE 0.043 0.002 PHE A 263 TYR 0.016 0.001 TYR B 291 ARG 0.004 0.001 ARG A 186 Details of bonding type rmsd link_NAG-ASN : bond 0.00817 ( 5) link_NAG-ASN : angle 5.27972 ( 15) link_BETA1-4 : bond 0.00493 ( 4) link_BETA1-4 : angle 2.81334 ( 12) hydrogen bonds : bond 0.03446 ( 184) hydrogen bonds : angle 6.48689 ( 462) SS BOND : bond 0.00299 ( 13) SS BOND : angle 0.80492 ( 26) covalent geometry : bond 0.00263 ( 6522) covalent geometry : angle 0.69832 ( 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 104 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8986 (tp30) cc_final: 0.8720 (tp30) REVERT: A 149 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8342 (mmtt) REVERT: A 157 LEU cc_start: 0.5326 (tp) cc_final: 0.5020 (tp) REVERT: B 46 MET cc_start: 0.7074 (mtt) cc_final: 0.6795 (mpp) REVERT: B 168 PHE cc_start: 0.4563 (OUTLIER) cc_final: 0.3328 (p90) REVERT: E 72 ASP cc_start: 0.7722 (t0) cc_final: 0.7391 (t0) REVERT: E 89 GLU cc_start: 0.8110 (pt0) cc_final: 0.7843 (pt0) REVERT: E 99 TYR cc_start: 0.3697 (OUTLIER) cc_final: 0.2616 (t80) REVERT: E 123 MET cc_start: 0.6967 (pmm) cc_final: 0.6342 (pmm) REVERT: E 125 MET cc_start: 0.6475 (pmm) cc_final: 0.6210 (pmm) REVERT: F 111 TYR cc_start: 0.5613 (OUTLIER) cc_final: 0.4596 (t80) REVERT: D 94 GLN cc_start: 0.5381 (OUTLIER) cc_final: 0.5063 (pt0) REVERT: G 108 ILE cc_start: 0.4508 (OUTLIER) cc_final: 0.3927 (pt) outliers start: 28 outliers final: 17 residues processed: 99 average time/residue: 0.1674 time to fit residues: 24.8990 Evaluate side-chains 98 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 GLN Chi-restraints excluded: chain A residue 214 ILE 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 168 PHE Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 22 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.105047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.093978 restraints weight = 42756.888| |-----------------------------------------------------------------------------| r_work (start): 0.4230 rms_B_bonded: 6.89 r_work (final): 0.4230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6544 Z= 0.148 Angle : 0.760 10.766 8924 Z= 0.369 Chirality : 0.046 0.408 1056 Planarity : 0.004 0.047 1106 Dihedral : 8.503 58.903 1211 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 4.53 % Allowed : 26.09 % 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: -1.95 (0.29), residues: 778 helix: -1.34 (0.44), residues: 117 sheet: -0.32 (0.38), residues: 178 loop : -1.73 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 59 HIS 0.004 0.001 HIS B 155 PHE 0.042 0.003 PHE A 263 TYR 0.018 0.001 TYR B 291 ARG 0.004 0.001 ARG F 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00754 ( 5) link_NAG-ASN : angle 5.22348 ( 15) link_BETA1-4 : bond 0.00423 ( 4) link_BETA1-4 : angle 2.87114 ( 12) hydrogen bonds : bond 0.03751 ( 184) hydrogen bonds : angle 6.56654 ( 462) SS BOND : bond 0.00436 ( 13) SS BOND : angle 1.03121 ( 26) covalent geometry : bond 0.00326 ( 6522) covalent geometry : angle 0.72181 ( 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 102 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9021 (tp30) cc_final: 0.8402 (tp30) REVERT: A 149 LYS cc_start: 0.8697 (tmtt) cc_final: 0.8405 (mmtt) REVERT: A 157 LEU cc_start: 0.5450 (tp) cc_final: 0.5162 (tp) REVERT: B 38 MET cc_start: 0.7443 (tpp) cc_final: 0.7235 (tpp) REVERT: B 168 PHE cc_start: 0.4626 (OUTLIER) cc_final: 0.3491 (p90) REVERT: E 72 ASP cc_start: 0.7795 (t0) cc_final: 0.7563 (t0) REVERT: E 89 GLU cc_start: 0.8170 (pt0) cc_final: 0.7703 (pt0) REVERT: E 99 TYR cc_start: 0.3789 (OUTLIER) cc_final: 0.2540 (t80) REVERT: E 123 MET cc_start: 0.7007 (pmm) cc_final: 0.6359 (pmm) REVERT: F 111 TYR cc_start: 0.5617 (OUTLIER) cc_final: 0.4687 (t80) REVERT: D 94 GLN cc_start: 0.5552 (OUTLIER) cc_final: 0.5340 (pt0) REVERT: G 108 ILE cc_start: 0.4735 (OUTLIER) cc_final: 0.4148 (pt) outliers start: 29 outliers final: 20 residues processed: 98 average time/residue: 0.2711 time to fit residues: 36.7339 Evaluate side-chains 97 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 214 ILE 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 168 PHE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain F residue 120 GLU Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE 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: 0.7980 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.4479 r_free = 0.4479 target = 0.106321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.095252 restraints weight = 42292.600| |-----------------------------------------------------------------------------| r_work (start): 0.4263 rms_B_bonded: 6.95 r_work (final): 0.4263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6544 Z= 0.126 Angle : 0.832 28.493 8924 Z= 0.382 Chirality : 0.046 0.404 1056 Planarity : 0.004 0.044 1106 Dihedral : 8.411 59.364 1211 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.17 % Favored : 93.70 % Rotamer: Outliers : 3.91 % Allowed : 26.72 % 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: -1.86 (0.29), residues: 778 helix: -1.24 (0.44), residues: 121 sheet: -0.36 (0.36), residues: 194 loop : -1.67 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 59 HIS 0.002 0.001 HIS B 155 PHE 0.043 0.002 PHE A 263 TYR 0.015 0.001 TYR B 291 ARG 0.015 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00857 ( 5) link_NAG-ASN : angle 9.69666 ( 15) link_BETA1-4 : bond 0.01412 ( 4) link_BETA1-4 : angle 3.33492 ( 12) hydrogen bonds : bond 0.03372 ( 184) hydrogen bonds : angle 6.39450 ( 462) SS BOND : bond 0.00323 ( 13) SS BOND : angle 0.87243 ( 26) covalent geometry : bond 0.00277 ( 6522) covalent geometry : angle 0.72087 ( 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 103 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9000 (tp30) cc_final: 0.8408 (tp30) REVERT: A 149 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8408 (mmtt) REVERT: A 157 LEU cc_start: 0.5432 (tp) cc_final: 0.5138 (tp) REVERT: A 188 MET cc_start: 0.8295 (ptt) cc_final: 0.7869 (ppp) REVERT: B 168 PHE cc_start: 0.4375 (OUTLIER) cc_final: 0.3320 (p90) REVERT: E 89 GLU cc_start: 0.8037 (pt0) cc_final: 0.7690 (pt0) REVERT: E 99 TYR cc_start: 0.3787 (OUTLIER) cc_final: 0.2430 (t80) REVERT: E 123 MET cc_start: 0.6954 (pmm) cc_final: 0.6577 (pmm) REVERT: F 111 TYR cc_start: 0.5648 (OUTLIER) cc_final: 0.4769 (t80) REVERT: D 94 GLN cc_start: 0.5125 (OUTLIER) cc_final: 0.4758 (pt0) REVERT: G 108 ILE cc_start: 0.4633 (OUTLIER) cc_final: 0.4051 (pt) outliers start: 25 outliers final: 18 residues processed: 100 average time/residue: 0.2058 time to fit residues: 29.6625 Evaluate side-chains 94 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 71 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE 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 168 PHE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 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 F residue 121 ASN Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 104 CYS Chi-restraints excluded: chain G residue 108 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 40 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.104793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.093888 restraints weight = 43357.100| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 6.87 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.3669 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= 0.152 Angle : 0.842 25.997 8924 Z= 0.392 Chirality : 0.046 0.407 1056 Planarity : 0.004 0.046 1106 Dihedral : 8.469 59.155 1211 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.46 % Favored : 92.42 % Rotamer: Outliers : 3.44 % Allowed : 27.19 % 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: -1.89 (0.29), residues: 778 helix: -1.25 (0.44), residues: 121 sheet: -0.28 (0.38), residues: 184 loop : -1.72 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 59 HIS 0.004 0.001 HIS B 155 PHE 0.050 0.003 PHE A 263 TYR 0.017 0.001 TYR B 291 ARG 0.006 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00755 ( 5) link_NAG-ASN : angle 9.18012 ( 15) link_BETA1-4 : bond 0.01079 ( 4) link_BETA1-4 : angle 3.30314 ( 12) hydrogen bonds : bond 0.03595 ( 184) hydrogen bonds : angle 6.51673 ( 462) SS BOND : bond 0.00436 ( 13) SS BOND : angle 1.05499 ( 26) covalent geometry : bond 0.00334 ( 6522) covalent geometry : angle 0.74296 ( 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 95 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.9037 (tp30) cc_final: 0.8483 (tp30) REVERT: A 149 LYS cc_start: 0.8657 (tmtt) cc_final: 0.8390 (mmtt) REVERT: A 157 LEU cc_start: 0.5407 (tp) cc_final: 0.5112 (tp) REVERT: A 188 MET cc_start: 0.8376 (ptt) cc_final: 0.7957 (ppp) REVERT: B 168 PHE cc_start: 0.4590 (OUTLIER) cc_final: 0.3529 (p90) REVERT: E 72 ASP cc_start: 0.7485 (t0) cc_final: 0.7241 (t0) REVERT: E 89 GLU cc_start: 0.7943 (pt0) cc_final: 0.7640 (pt0) REVERT: E 99 TYR cc_start: 0.3787 (OUTLIER) cc_final: 0.2465 (t80) REVERT: E 123 MET cc_start: 0.6908 (pmm) cc_final: 0.6528 (pmm) REVERT: F 111 TYR cc_start: 0.5698 (OUTLIER) cc_final: 0.4838 (t80) REVERT: D 94 GLN cc_start: 0.5636 (OUTLIER) cc_final: 0.5421 (pt0) REVERT: G 108 ILE cc_start: 0.4639 (OUTLIER) cc_final: 0.4068 (pt) outliers start: 22 outliers final: 16 residues processed: 91 average time/residue: 0.1662 time to fit residues: 22.4288 Evaluate side-chains 94 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 ILE 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 168 PHE Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 206 TYR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain E residue 99 TYR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 111 TYR Chi-restraints excluded: chain D residue 43 TRP Chi-restraints excluded: chain D residue 93 CYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain G residue 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: 2.9990 chunk 48 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 46 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.102677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.091911 restraints weight = 43906.628| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 6.59 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6544 Z= 0.170 Angle : 0.837 20.485 8924 Z= 0.399 Chirality : 0.046 0.417 1056 Planarity : 0.005 0.051 1106 Dihedral : 8.679 57.041 1211 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.46 % Favored : 92.42 % Rotamer: Outliers : 3.59 % Allowed : 27.34 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.29), residues: 778 helix: -1.12 (0.45), residues: 120 sheet: -0.47 (0.36), residues: 201 loop : -1.68 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 59 HIS 0.004 0.001 HIS B 155 PHE 0.052 0.003 PHE A 263 TYR 0.019 0.002 TYR B 291 ARG 0.007 0.001 ARG E 117 Details of bonding type rmsd link_NAG-ASN : bond 0.00604 ( 5) link_NAG-ASN : angle 7.56643 ( 15) link_BETA1-4 : bond 0.00873 ( 4) link_BETA1-4 : angle 3.19745 ( 12) hydrogen bonds : bond 0.03778 ( 184) hydrogen bonds : angle 6.73486 ( 462) SS BOND : bond 0.00540 ( 13) SS BOND : angle 1.17788 ( 26) covalent geometry : bond 0.00374 ( 6522) covalent geometry : angle 0.76811 ( 8871) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3896.16 seconds wall clock time: 70 minutes 2.57 seconds (4202.57 seconds total)