Starting phenix.real_space_refine on Fri Dec 27 21:21:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqf_25383/12_2024/7sqf_25383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqf_25383/12_2024/7sqf_25383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sqf_25383/12_2024/7sqf_25383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqf_25383/12_2024/7sqf_25383.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqf_25383/12_2024/7sqf_25383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqf_25383/12_2024/7sqf_25383.cif" } resolution = 3.1 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= 0.000 sd= 0.013 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 27 5.16 5 C 4296 2.51 5 N 1089 2.21 5 O 1218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6630 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2154 Classifications: {'peptide': 273} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 13, 'TRANS': 259} Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Restraints were copied for chains: C, B Time building chain proxies: 4.77, per 1000 atoms: 0.72 Number of scatterers: 6630 At special positions: 0 Unit cell: (80.2481, 82.73, 122.44, 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 27 16.00 O 1218 8.00 N 1089 7.00 C 4296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 NAG-ASN " NAG A 401 " - " ASN A 148 " " NAG A 402 " - " ASN A 162 " " NAG A 403 " - " ASN A 190 " " NAG A 404 " - " ASN A 155 " " NAG B 401 " - " ASN B 148 " " NAG B 402 " - " ASN B 162 " " NAG B 403 " - " ASN B 190 " " NAG B 404 " - " ASN B 155 " " NAG C 401 " - " ASN C 148 " " NAG C 402 " - " ASN C 162 " " NAG C 403 " - " ASN C 190 " " NAG C 404 " - " ASN C 155 " Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 1.2 seconds 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1578 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 36.0% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 65 through 98 removed outlier: 4.047A pdb=" N LEU A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 302 through 337 Processing helix chain 'B' and resid 66 through 98 Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 217 through 226 Processing helix chain 'B' and resid 272 through 276 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 302 through 337 Processing helix chain 'C' and resid 66 through 98 Processing helix chain 'C' and resid 206 through 213 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 272 through 276 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 302 through 337 Processing sheet with id=AA1, first strand: chain 'A' and resid 100 through 107 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 100 through 107 current: chain 'A' and resid 165 through 172 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 165 through 172 current: chain 'A' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 229 through 233 current: chain 'A' and resid 254 through 267 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 254 through 267 current: chain 'B' and resid 165 through 172 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 165 through 172 current: chain 'B' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 229 through 233 current: chain 'B' and resid 254 through 267 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 254 through 267 current: chain 'C' and resid 165 through 172 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 165 through 172 current: chain 'C' and resid 229 through 233 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 229 through 233 current: chain 'C' and resid 254 through 267 No H-bonds generated for sheet with id=AA1 225 hydrogen bonds defined for protein. 657 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: 1.47 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2058 1.34 - 1.46: 1607 1.46 - 1.58: 3088 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 6795 Sorted by residual: bond pdb=" N GLU C 133 " pdb=" CA GLU C 133 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.14e+01 bond pdb=" N GLU A 133 " pdb=" CA GLU A 133 " ideal model delta sigma weight residual 1.457 1.501 -0.043 1.29e-02 6.01e+03 1.13e+01 bond pdb=" N GLU B 133 " pdb=" CA GLU B 133 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.11e+01 bond pdb=" N LYS A 231 " pdb=" CA LYS A 231 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.55e+00 bond pdb=" N LYS C 231 " pdb=" CA LYS C 231 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.25e-02 6.40e+03 7.53e+00 ... (remaining 6790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 8676 1.12 - 2.24: 396 2.24 - 3.36: 133 3.36 - 4.47: 17 4.47 - 5.59: 6 Bond angle restraints: 9228 Sorted by residual: angle pdb=" CA ASP A 269 " pdb=" CB ASP A 269 " pdb=" CG ASP A 269 " ideal model delta sigma weight residual 112.60 116.15 -3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP C 269 " pdb=" CB ASP C 269 " pdb=" CG ASP C 269 " ideal model delta sigma weight residual 112.60 116.15 -3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" CA ASP B 269 " pdb=" CB ASP B 269 " pdb=" CG ASP B 269 " ideal model delta sigma weight residual 112.60 116.11 -3.51 1.00e+00 1.00e+00 1.23e+01 angle pdb=" N GLU B 94 " pdb=" CA GLU B 94 " pdb=" CB GLU B 94 " ideal model delta sigma weight residual 110.28 115.03 -4.75 1.55e+00 4.16e-01 9.39e+00 angle pdb=" CA ASN C 215 " pdb=" C ASN C 215 " pdb=" O ASN C 215 " ideal model delta sigma weight residual 120.24 116.85 3.39 1.11e+00 8.12e-01 9.35e+00 ... (remaining 9223 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 3834 17.35 - 34.70: 279 34.70 - 52.05: 57 52.05 - 69.40: 24 69.40 - 86.75: 6 Dihedral angle restraints: 4200 sinusoidal: 1776 harmonic: 2424 Sorted by residual: dihedral pdb=" CA PHE A 258 " pdb=" C PHE A 258 " pdb=" N ARG A 259 " pdb=" CA ARG A 259 " ideal model delta harmonic sigma weight residual 180.00 163.75 16.25 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PHE C 258 " pdb=" C PHE C 258 " pdb=" N ARG C 259 " pdb=" CA ARG C 259 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA PHE B 258 " pdb=" C PHE B 258 " pdb=" N ARG B 259 " pdb=" CA ARG B 259 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 4197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 936 0.068 - 0.136: 114 0.136 - 0.203: 9 0.203 - 0.271: 0 0.271 - 0.339: 3 Chirality restraints: 1062 Sorted by residual: chirality pdb=" C1 NAG C 402 " pdb=" ND2 ASN C 162 " pdb=" C2 NAG C 402 " pdb=" O5 NAG C 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 NAG B 402 " pdb=" ND2 ASN B 162 " pdb=" C2 NAG B 402 " pdb=" O5 NAG B 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.86e+00 chirality pdb=" C1 NAG A 402 " pdb=" ND2 ASN A 162 " pdb=" C2 NAG A 402 " pdb=" O5 NAG A 402 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 1059 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 148 " -0.003 2.00e-02 2.50e+03 1.74e-02 3.77e+00 pdb=" CG ASN B 148 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 148 " -0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN B 148 " 0.014 2.00e-02 2.50e+03 pdb=" C1 NAG B 401 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 148 " 0.003 2.00e-02 2.50e+03 1.74e-02 3.77e+00 pdb=" CG ASN C 148 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN C 148 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN C 148 " -0.014 2.00e-02 2.50e+03 pdb=" C1 NAG C 401 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 148 " 0.003 2.00e-02 2.50e+03 1.73e-02 3.73e+00 pdb=" CG ASN A 148 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 148 " 0.021 2.00e-02 2.50e+03 pdb=" ND2 ASN A 148 " -0.013 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.015 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 2671 2.91 - 3.41: 6176 3.41 - 3.90: 11174 3.90 - 4.40: 12569 4.40 - 4.90: 20489 Nonbonded interactions: 53079 Sorted by model distance: nonbonded pdb=" O THR B 90 " pdb=" OE1 GLU B 94 " model vdw 2.409 3.040 nonbonded pdb=" O THR C 90 " pdb=" OE1 GLU C 94 " model vdw 2.409 3.040 nonbonded pdb=" O THR A 90 " pdb=" OE1 GLU A 94 " model vdw 2.409 3.040 nonbonded pdb=" OH TYR A 156 " pdb=" OE1 GLU A 224 " model vdw 2.475 3.040 nonbonded pdb=" OH TYR B 156 " pdb=" OE1 GLU B 224 " model vdw 2.475 3.040 ... (remaining 53074 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 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 18.920 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 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 : 0.005 0.043 6795 Z= 0.302 Angle : 0.602 5.593 9228 Z= 0.342 Chirality : 0.048 0.339 1062 Planarity : 0.004 0.029 1158 Dihedral : 13.840 86.752 2622 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.39 (0.29), residues: 813 helix: 2.71 (0.29), residues: 279 sheet: 0.39 (0.28), residues: 315 loop : -0.58 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 287 HIS 0.002 0.001 HIS C 130 PHE 0.012 0.002 PHE B 204 TYR 0.026 0.002 TYR A 111 ARG 0.001 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ILE cc_start: 0.8386 (mt) cc_final: 0.8125 (mm) REVERT: A 75 LEU cc_start: 0.8258 (mt) cc_final: 0.7905 (mm) REVERT: A 86 TYR cc_start: 0.7086 (t80) cc_final: 0.6754 (t80) REVERT: A 87 ARG cc_start: 0.7548 (tpp-160) cc_final: 0.6993 (tpt-90) REVERT: A 90 THR cc_start: 0.7730 (m) cc_final: 0.6830 (p) REVERT: A 93 ARG cc_start: 0.7819 (ttt180) cc_final: 0.7418 (ttt180) REVERT: A 94 GLU cc_start: 0.7320 (mp0) cc_final: 0.6693 (mp0) REVERT: A 106 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7669 (ttmt) REVERT: A 292 ILE cc_start: 0.8082 (mt) cc_final: 0.7863 (mt) REVERT: A 294 LYS cc_start: 0.8845 (mttp) cc_final: 0.8615 (mmtp) REVERT: A 306 THR cc_start: 0.7355 (m) cc_final: 0.6982 (p) REVERT: A 314 PHE cc_start: 0.8333 (t80) cc_final: 0.8077 (t80) REVERT: B 71 ILE cc_start: 0.8425 (mt) cc_final: 0.8146 (mm) REVERT: B 73 ILE cc_start: 0.8006 (mm) cc_final: 0.7800 (mm) REVERT: B 75 LEU cc_start: 0.8256 (mt) cc_final: 0.7952 (mm) REVERT: B 94 GLU cc_start: 0.7548 (mp0) cc_final: 0.6719 (mp0) REVERT: B 96 LEU cc_start: 0.8735 (mt) cc_final: 0.8515 (mt) REVERT: B 106 LYS cc_start: 0.7898 (ttpt) cc_final: 0.7664 (ptmt) REVERT: B 292 ILE cc_start: 0.8056 (mt) cc_final: 0.7843 (mt) REVERT: C 80 VAL cc_start: 0.8169 (t) cc_final: 0.7969 (p) REVERT: C 92 PHE cc_start: 0.8279 (t80) cc_final: 0.8047 (t80) REVERT: C 94 GLU cc_start: 0.7428 (mp0) cc_final: 0.6689 (mp0) REVERT: C 95 LYS cc_start: 0.8535 (mttt) cc_final: 0.8332 (ttmm) REVERT: C 96 LEU cc_start: 0.8886 (mt) cc_final: 0.8526 (mp) REVERT: C 106 LYS cc_start: 0.7794 (ttpt) cc_final: 0.7314 (ttmm) REVERT: C 206 SER cc_start: 0.7842 (p) cc_final: 0.7619 (p) REVERT: C 249 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7261 (mt-10) REVERT: C 314 PHE cc_start: 0.8337 (t80) cc_final: 0.7946 (t80) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.3157 time to fit residues: 100.2976 Evaluate side-chains 242 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 208 GLN B 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6795 Z= 0.366 Angle : 0.590 10.611 9228 Z= 0.310 Chirality : 0.048 0.330 1062 Planarity : 0.004 0.031 1158 Dihedral : 6.345 50.896 1134 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.18 % Allowed : 11.65 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.45 (0.29), residues: 813 helix: 2.84 (0.29), residues: 282 sheet: 0.39 (0.28), residues: 318 loop : -0.67 (0.42), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.005 0.002 HIS C 130 PHE 0.018 0.002 PHE C 232 TYR 0.013 0.002 TYR B 119 ARG 0.008 0.001 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 257 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8375 (mt) cc_final: 0.8108 (mm) REVERT: A 93 ARG cc_start: 0.7988 (ttt180) cc_final: 0.7562 (ttt180) REVERT: A 94 GLU cc_start: 0.7534 (mp0) cc_final: 0.6619 (mp0) REVERT: A 101 MET cc_start: 0.8907 (mtt) cc_final: 0.8620 (mtt) REVERT: A 106 LYS cc_start: 0.7846 (ttpt) cc_final: 0.7511 (ptmt) REVERT: A 294 LYS cc_start: 0.8835 (mttp) cc_final: 0.8512 (mttm) REVERT: A 306 THR cc_start: 0.7353 (m) cc_final: 0.6927 (p) REVERT: A 314 PHE cc_start: 0.8396 (t80) cc_final: 0.8090 (t80) REVERT: B 92 PHE cc_start: 0.8617 (t80) cc_final: 0.8244 (t80) REVERT: B 94 GLU cc_start: 0.7599 (mp0) cc_final: 0.6616 (mp0) REVERT: B 96 LEU cc_start: 0.8749 (mt) cc_final: 0.8397 (mt) REVERT: B 106 LYS cc_start: 0.7858 (ttpt) cc_final: 0.7486 (ptmt) REVERT: B 188 ARG cc_start: 0.8538 (tmm-80) cc_final: 0.8262 (ttt-90) REVERT: B 297 ASP cc_start: 0.7403 (p0) cc_final: 0.7167 (p0) REVERT: B 306 THR cc_start: 0.7487 (m) cc_final: 0.7056 (p) REVERT: C 71 ILE cc_start: 0.8345 (mt) cc_final: 0.8069 (mp) REVERT: C 75 LEU cc_start: 0.8222 (mt) cc_final: 0.7920 (mt) REVERT: C 87 ARG cc_start: 0.7569 (tpt-90) cc_final: 0.7226 (tpt-90) REVERT: C 92 PHE cc_start: 0.8479 (t80) cc_final: 0.8244 (t80) REVERT: C 96 LEU cc_start: 0.8749 (mt) cc_final: 0.8343 (mp) REVERT: C 106 LYS cc_start: 0.7763 (ttpt) cc_final: 0.7317 (ttpp) REVERT: C 243 SER cc_start: 0.8696 (m) cc_final: 0.8430 (p) REVERT: C 260 GLN cc_start: 0.7573 (pt0) cc_final: 0.7264 (pt0) REVERT: C 297 ASP cc_start: 0.7117 (p0) cc_final: 0.6593 (p0) REVERT: C 314 PHE cc_start: 0.8390 (t80) cc_final: 0.7972 (t80) outliers start: 8 outliers final: 4 residues processed: 261 average time/residue: 0.2898 time to fit residues: 90.6445 Evaluate side-chains 251 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 247 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain C residue 104 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 0.4980 chunk 61 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6795 Z= 0.282 Angle : 0.519 5.620 9228 Z= 0.278 Chirality : 0.047 0.333 1062 Planarity : 0.003 0.028 1158 Dihedral : 5.472 59.522 1134 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.95 % Allowed : 14.45 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.44 (0.30), residues: 813 helix: 2.95 (0.29), residues: 282 sheet: 0.36 (0.29), residues: 315 loop : -0.81 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.003 0.001 HIS C 130 PHE 0.019 0.002 PHE B 314 TYR 0.011 0.002 TYR B 227 ARG 0.003 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 243 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8424 (mt) cc_final: 0.8150 (mm) REVERT: A 90 THR cc_start: 0.7959 (m) cc_final: 0.7656 (p) REVERT: A 92 PHE cc_start: 0.8674 (t80) cc_final: 0.8408 (t80) REVERT: A 93 ARG cc_start: 0.8083 (ttt180) cc_final: 0.7651 (ttt180) REVERT: A 101 MET cc_start: 0.8945 (mtt) cc_final: 0.8675 (mtt) REVERT: A 106 LYS cc_start: 0.7828 (ttpt) cc_final: 0.7590 (tptp) REVERT: A 306 THR cc_start: 0.7352 (m) cc_final: 0.6931 (p) REVERT: A 314 PHE cc_start: 0.8382 (t80) cc_final: 0.8062 (t80) REVERT: B 83 PHE cc_start: 0.8861 (t80) cc_final: 0.8648 (t80) REVERT: B 92 PHE cc_start: 0.8712 (t80) cc_final: 0.8363 (t80) REVERT: B 95 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8303 (mtmm) REVERT: B 96 LEU cc_start: 0.8758 (mt) cc_final: 0.8396 (mt) REVERT: B 106 LYS cc_start: 0.7880 (ttpt) cc_final: 0.7586 (ptmt) REVERT: B 297 ASP cc_start: 0.7421 (p0) cc_final: 0.7195 (p0) REVERT: B 306 THR cc_start: 0.7518 (m) cc_final: 0.7143 (p) REVERT: C 80 VAL cc_start: 0.8201 (t) cc_final: 0.7944 (p) REVERT: C 87 ARG cc_start: 0.7575 (tpt-90) cc_final: 0.7327 (tpt-90) REVERT: C 95 LYS cc_start: 0.8581 (mttt) cc_final: 0.8321 (ttmm) REVERT: C 243 SER cc_start: 0.8623 (m) cc_final: 0.8387 (p) REVERT: C 297 ASP cc_start: 0.7024 (p0) cc_final: 0.6207 (p0) REVERT: C 314 PHE cc_start: 0.8380 (t80) cc_final: 0.7925 (t80) outliers start: 20 outliers final: 14 residues processed: 251 average time/residue: 0.3096 time to fit residues: 92.4626 Evaluate side-chains 254 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 239 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 124 GLN Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 104 SER Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 208 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6795 Z= 0.277 Angle : 0.533 6.905 9228 Z= 0.286 Chirality : 0.047 0.333 1062 Planarity : 0.003 0.024 1158 Dihedral : 5.855 56.962 1134 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.65 % Allowed : 18.44 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.30), residues: 813 helix: 2.86 (0.28), residues: 282 sheet: 0.27 (0.30), residues: 315 loop : -0.79 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.003 0.001 HIS B 130 PHE 0.017 0.002 PHE C 92 TYR 0.015 0.001 TYR B 227 ARG 0.005 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 239 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8014 (m) cc_final: 0.7667 (p) REVERT: A 92 PHE cc_start: 0.8733 (t80) cc_final: 0.8423 (t80) REVERT: A 93 ARG cc_start: 0.8103 (ttt180) cc_final: 0.7662 (ttt180) REVERT: A 101 MET cc_start: 0.8952 (mtt) cc_final: 0.8739 (mtt) REVERT: A 106 LYS cc_start: 0.7854 (ttpt) cc_final: 0.7612 (tptp) REVERT: A 306 THR cc_start: 0.7354 (m) cc_final: 0.6957 (p) REVERT: A 314 PHE cc_start: 0.8386 (t80) cc_final: 0.8066 (t80) REVERT: B 92 PHE cc_start: 0.8745 (t80) cc_final: 0.8407 (t80) REVERT: B 95 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8287 (mtmm) REVERT: B 96 LEU cc_start: 0.8717 (mt) cc_final: 0.8358 (mt) REVERT: B 106 LYS cc_start: 0.7864 (ttpt) cc_final: 0.7564 (ptmt) REVERT: B 306 THR cc_start: 0.7421 (m) cc_final: 0.7100 (p) REVERT: B 318 PHE cc_start: 0.8461 (t80) cc_final: 0.8190 (t80) REVERT: C 75 LEU cc_start: 0.8287 (mt) cc_final: 0.8026 (mm) REVERT: C 80 VAL cc_start: 0.8211 (t) cc_final: 0.7938 (p) REVERT: C 95 LYS cc_start: 0.8602 (mttt) cc_final: 0.8334 (ttmm) REVERT: C 176 GLU cc_start: 0.7205 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: C 243 SER cc_start: 0.8611 (m) cc_final: 0.8378 (p) REVERT: C 297 ASP cc_start: 0.7038 (p0) cc_final: 0.6225 (p0) REVERT: C 314 PHE cc_start: 0.8378 (t80) cc_final: 0.7925 (t80) outliers start: 18 outliers final: 13 residues processed: 244 average time/residue: 0.3101 time to fit residues: 89.8662 Evaluate side-chains 254 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 239 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 0.3980 chunk 0 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6795 Z= 0.249 Angle : 0.508 5.313 9228 Z= 0.277 Chirality : 0.045 0.333 1062 Planarity : 0.003 0.023 1158 Dihedral : 5.136 55.780 1134 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.10 % Allowed : 19.17 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.24 (0.30), residues: 813 helix: 2.79 (0.29), residues: 282 sheet: 0.16 (0.30), residues: 315 loop : -0.75 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.002 0.001 HIS B 130 PHE 0.017 0.002 PHE C 160 TYR 0.010 0.001 TYR A 201 ARG 0.004 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.7984 (m) cc_final: 0.7649 (p) REVERT: A 92 PHE cc_start: 0.8754 (t80) cc_final: 0.8437 (t80) REVERT: A 93 ARG cc_start: 0.8138 (ttt180) cc_final: 0.7679 (ttt180) REVERT: A 101 MET cc_start: 0.8952 (mtt) cc_final: 0.8750 (mtt) REVERT: A 106 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7631 (ttpt) REVERT: A 209 GLU cc_start: 0.6834 (pt0) cc_final: 0.6626 (pt0) REVERT: A 314 PHE cc_start: 0.8406 (t80) cc_final: 0.8100 (t80) REVERT: B 92 PHE cc_start: 0.8728 (t80) cc_final: 0.8401 (t80) REVERT: B 96 LEU cc_start: 0.8719 (mt) cc_final: 0.8374 (mt) REVERT: B 106 LYS cc_start: 0.7877 (ttpt) cc_final: 0.7535 (ptmt) REVERT: B 306 THR cc_start: 0.7558 (m) cc_final: 0.7193 (p) REVERT: B 318 PHE cc_start: 0.8458 (t80) cc_final: 0.8176 (t80) REVERT: C 75 LEU cc_start: 0.8300 (mt) cc_final: 0.8057 (mm) REVERT: C 80 VAL cc_start: 0.8215 (t) cc_final: 0.7934 (p) REVERT: C 94 GLU cc_start: 0.7457 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: C 95 LYS cc_start: 0.8615 (mttt) cc_final: 0.8328 (ttmm) REVERT: C 243 SER cc_start: 0.8625 (m) cc_final: 0.8370 (p) REVERT: C 297 ASP cc_start: 0.7061 (p0) cc_final: 0.6245 (p0) REVERT: C 314 PHE cc_start: 0.8364 (t80) cc_final: 0.7917 (t80) outliers start: 21 outliers final: 11 residues processed: 244 average time/residue: 0.3087 time to fit residues: 89.8039 Evaluate side-chains 242 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 230 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 GLN C 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6795 Z= 0.306 Angle : 0.525 4.992 9228 Z= 0.287 Chirality : 0.046 0.336 1062 Planarity : 0.003 0.022 1158 Dihedral : 4.857 40.929 1134 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.24 % Allowed : 20.80 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.30), residues: 813 helix: 2.65 (0.28), residues: 282 sheet: -0.06 (0.29), residues: 324 loop : -0.67 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 PHE 0.016 0.002 PHE C 232 TYR 0.009 0.001 TYR A 201 ARG 0.005 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8469 (mt) cc_final: 0.8204 (mm) REVERT: A 93 ARG cc_start: 0.8141 (ttt180) cc_final: 0.7694 (ttt180) REVERT: A 106 LYS cc_start: 0.7823 (ttpt) cc_final: 0.7609 (ttpt) REVERT: A 249 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7481 (mp0) REVERT: A 314 PHE cc_start: 0.8425 (t80) cc_final: 0.8105 (t80) REVERT: B 92 PHE cc_start: 0.8724 (t80) cc_final: 0.8450 (t80) REVERT: B 94 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6615 (mp0) REVERT: B 96 LEU cc_start: 0.8701 (mt) cc_final: 0.8346 (mt) REVERT: B 106 LYS cc_start: 0.7829 (ttpt) cc_final: 0.7508 (ptmt) REVERT: B 306 THR cc_start: 0.7542 (m) cc_final: 0.7202 (p) REVERT: B 318 PHE cc_start: 0.8483 (t80) cc_final: 0.8206 (t80) REVERT: C 75 LEU cc_start: 0.8354 (mt) cc_final: 0.8131 (mm) REVERT: C 80 VAL cc_start: 0.8210 (t) cc_final: 0.7926 (p) REVERT: C 94 GLU cc_start: 0.7435 (OUTLIER) cc_final: 0.6553 (mp0) REVERT: C 95 LYS cc_start: 0.8640 (mttt) cc_final: 0.8329 (ttmm) REVERT: C 243 SER cc_start: 0.8594 (m) cc_final: 0.8354 (p) REVERT: C 297 ASP cc_start: 0.7037 (p0) cc_final: 0.6253 (p0) REVERT: C 314 PHE cc_start: 0.8381 (t80) cc_final: 0.7921 (t80) outliers start: 22 outliers final: 15 residues processed: 248 average time/residue: 0.3035 time to fit residues: 89.8233 Evaluate side-chains 254 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 237 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6795 Z= 0.353 Angle : 0.563 8.433 9228 Z= 0.308 Chirality : 0.046 0.337 1062 Planarity : 0.003 0.023 1158 Dihedral : 4.930 41.691 1134 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.54 % Allowed : 21.39 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.95 (0.30), residues: 813 helix: 2.53 (0.29), residues: 279 sheet: -0.20 (0.29), residues: 324 loop : -0.47 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.004 0.001 HIS B 98 PHE 0.019 0.002 PHE A 232 TYR 0.010 0.002 TYR B 111 ARG 0.005 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 241 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.8170 (ttt180) cc_final: 0.7693 (ttt180) REVERT: A 94 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: A 106 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7565 (tptp) REVERT: A 249 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7493 (mp0) REVERT: A 314 PHE cc_start: 0.8435 (t80) cc_final: 0.8134 (t80) REVERT: B 92 PHE cc_start: 0.8731 (t80) cc_final: 0.8518 (t80) REVERT: B 94 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: B 96 LEU cc_start: 0.8725 (mt) cc_final: 0.8374 (mt) REVERT: B 318 PHE cc_start: 0.8483 (t80) cc_final: 0.8230 (t80) REVERT: C 75 LEU cc_start: 0.8415 (mt) cc_final: 0.8192 (mm) REVERT: C 80 VAL cc_start: 0.8219 (t) cc_final: 0.7926 (p) REVERT: C 87 ARG cc_start: 0.7751 (tpt-90) cc_final: 0.7406 (tpt-90) REVERT: C 94 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: C 95 LYS cc_start: 0.8622 (mttt) cc_final: 0.8316 (ttmm) REVERT: C 243 SER cc_start: 0.8603 (m) cc_final: 0.8330 (p) REVERT: C 297 ASP cc_start: 0.7043 (p0) cc_final: 0.6265 (p0) REVERT: C 314 PHE cc_start: 0.8385 (t80) cc_final: 0.7920 (t80) outliers start: 24 outliers final: 18 residues processed: 250 average time/residue: 0.3110 time to fit residues: 92.8058 Evaluate side-chains 261 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 240 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.0770 chunk 49 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 0.0470 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 72 optimal weight: 0.0870 chunk 43 optimal weight: 0.9980 overall best weight: 0.2014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS B 266 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6795 Z= 0.166 Angle : 0.504 8.662 9228 Z= 0.272 Chirality : 0.045 0.330 1062 Planarity : 0.003 0.025 1158 Dihedral : 4.506 36.941 1134 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.80 % Allowed : 22.57 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.31), residues: 813 helix: 2.66 (0.29), residues: 279 sheet: -0.21 (0.29), residues: 324 loop : -0.34 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 230 HIS 0.004 0.001 HIS B 98 PHE 0.013 0.001 PHE A 92 TYR 0.012 0.001 TYR A 201 ARG 0.002 0.000 ARG C 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8158 (mm) REVERT: A 92 PHE cc_start: 0.8717 (t80) cc_final: 0.8506 (t80) REVERT: A 93 ARG cc_start: 0.8150 (ttt180) cc_final: 0.7677 (ttt180) REVERT: A 94 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6438 (mp0) REVERT: A 106 LYS cc_start: 0.7815 (ttpt) cc_final: 0.7592 (tptp) REVERT: A 260 GLN cc_start: 0.7687 (pt0) cc_final: 0.7366 (pt0) REVERT: A 306 THR cc_start: 0.7365 (m) cc_final: 0.6963 (p) REVERT: A 314 PHE cc_start: 0.8390 (t80) cc_final: 0.8037 (t80) REVERT: B 92 PHE cc_start: 0.8738 (t80) cc_final: 0.8521 (t80) REVERT: B 94 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: B 97 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7936 (ttmt) REVERT: B 318 PHE cc_start: 0.8390 (t80) cc_final: 0.8135 (t80) REVERT: C 80 VAL cc_start: 0.8185 (t) cc_final: 0.7895 (p) REVERT: C 87 ARG cc_start: 0.7719 (tpt-90) cc_final: 0.7384 (tpt-90) REVERT: C 94 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: C 95 LYS cc_start: 0.8601 (mttt) cc_final: 0.8300 (ttmm) REVERT: C 179 LYS cc_start: 0.7852 (mttp) cc_final: 0.7475 (mttp) REVERT: C 314 PHE cc_start: 0.8339 (t80) cc_final: 0.7845 (t80) outliers start: 19 outliers final: 10 residues processed: 253 average time/residue: 0.3005 time to fit residues: 91.0321 Evaluate side-chains 252 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 65 optimal weight: 0.6980 chunk 68 optimal weight: 0.1980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 76 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS B 143 GLN B 221 GLN C 260 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6795 Z= 0.284 Angle : 0.597 8.915 9228 Z= 0.317 Chirality : 0.050 0.614 1062 Planarity : 0.003 0.027 1158 Dihedral : 5.772 56.599 1134 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.10 % Allowed : 23.45 % Favored : 73.45 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.31), residues: 813 helix: 2.62 (0.29), residues: 279 sheet: -0.24 (0.29), residues: 327 loop : -0.26 (0.47), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.003 0.001 HIS B 98 PHE 0.025 0.002 PHE A 83 TYR 0.010 0.001 TYR A 132 ARG 0.002 0.000 ARG B 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 243 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8093 (mm) REVERT: A 78 MET cc_start: 0.8010 (tmm) cc_final: 0.7651 (tmm) REVERT: A 93 ARG cc_start: 0.8159 (ttt180) cc_final: 0.7692 (ttt180) REVERT: A 94 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: A 106 LYS cc_start: 0.7812 (ttpt) cc_final: 0.7564 (tptp) REVERT: A 314 PHE cc_start: 0.8416 (t80) cc_final: 0.8089 (t80) REVERT: B 92 PHE cc_start: 0.8756 (t80) cc_final: 0.8494 (t80) REVERT: B 94 GLU cc_start: 0.7459 (OUTLIER) cc_final: 0.6590 (mp0) REVERT: B 96 LEU cc_start: 0.8663 (mt) cc_final: 0.8346 (mt) REVERT: B 97 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7956 (ttmt) REVERT: B 306 THR cc_start: 0.7494 (m) cc_final: 0.7166 (p) REVERT: B 318 PHE cc_start: 0.8433 (t80) cc_final: 0.8175 (t80) REVERT: C 80 VAL cc_start: 0.8217 (t) cc_final: 0.7925 (p) REVERT: C 87 ARG cc_start: 0.7763 (tpt-90) cc_final: 0.7394 (tpt-90) REVERT: C 94 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: C 95 LYS cc_start: 0.8584 (mttt) cc_final: 0.8304 (ttmm) REVERT: C 243 SER cc_start: 0.8618 (m) cc_final: 0.8412 (p) REVERT: C 297 ASP cc_start: 0.7245 (p0) cc_final: 0.6725 (p0) REVERT: C 314 PHE cc_start: 0.8372 (t80) cc_final: 0.7891 (t80) outliers start: 21 outliers final: 15 residues processed: 248 average time/residue: 0.2920 time to fit residues: 87.0682 Evaluate side-chains 259 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 240 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 49 optimal weight: 0.0050 chunk 39 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 68 optimal weight: 0.0970 chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 0.0020 chunk 9 optimal weight: 2.9990 overall best weight: 0.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6795 Z= 0.205 Angle : 0.575 10.134 9228 Z= 0.307 Chirality : 0.048 0.432 1062 Planarity : 0.003 0.030 1158 Dihedral : 5.280 47.883 1134 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.80 % Allowed : 23.75 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.30), residues: 813 helix: 2.58 (0.29), residues: 279 sheet: -0.25 (0.29), residues: 327 loop : -0.25 (0.47), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.008 0.001 HIS B 98 PHE 0.016 0.001 PHE A 92 TYR 0.009 0.001 TYR A 132 ARG 0.001 0.000 ARG B 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1626 Ramachandran restraints generated. 813 Oldfield, 0 Emsley, 813 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 78 MET cc_start: 0.7983 (tmm) cc_final: 0.7609 (tmm) REVERT: A 93 ARG cc_start: 0.8163 (ttt180) cc_final: 0.7690 (ttt180) REVERT: A 94 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: A 106 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7581 (tptp) REVERT: A 172 GLN cc_start: 0.8533 (tt0) cc_final: 0.8308 (tt0) REVERT: A 314 PHE cc_start: 0.8402 (t80) cc_final: 0.8050 (t80) REVERT: B 92 PHE cc_start: 0.8744 (t80) cc_final: 0.8535 (t80) REVERT: B 94 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: B 97 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7992 (ttmt) REVERT: B 306 THR cc_start: 0.7491 (m) cc_final: 0.7162 (p) REVERT: B 318 PHE cc_start: 0.8392 (t80) cc_final: 0.8138 (t80) REVERT: C 80 VAL cc_start: 0.8187 (t) cc_final: 0.7898 (p) REVERT: C 87 ARG cc_start: 0.7743 (tpt-90) cc_final: 0.7392 (tpt-90) REVERT: C 94 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6501 (mp0) REVERT: C 95 LYS cc_start: 0.8564 (mttt) cc_final: 0.8295 (ttmm) REVERT: C 241 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8268 (mtpp) REVERT: C 297 ASP cc_start: 0.7159 (p0) cc_final: 0.6514 (p0) REVERT: C 314 PHE cc_start: 0.8348 (t80) cc_final: 0.7851 (t80) outliers start: 19 outliers final: 13 residues processed: 238 average time/residue: 0.2907 time to fit residues: 83.2102 Evaluate side-chains 250 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain B residue 71 ILE Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 95 LYS Chi-restraints excluded: chain B residue 107 GLU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 248 LYS Chi-restraints excluded: chain C residue 279 GLN Chi-restraints excluded: chain C residue 299 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9990 chunk 64 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.0030 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 43 optimal weight: 0.0370 overall best weight: 0.2468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.125588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.112629 restraints weight = 12744.701| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 2.86 r_work: 0.3459 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6795 Z= 0.185 Angle : 0.540 9.883 9228 Z= 0.291 Chirality : 0.046 0.328 1062 Planarity : 0.003 0.026 1158 Dihedral : 4.977 58.919 1134 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.36 % Allowed : 24.78 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.10 (0.31), residues: 813 helix: 2.63 (0.29), residues: 279 sheet: -0.19 (0.29), residues: 327 loop : -0.19 (0.47), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 230 HIS 0.006 0.001 HIS B 98 PHE 0.013 0.001 PHE C 232 TYR 0.007 0.001 TYR A 132 ARG 0.002 0.000 ARG A 180 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2535.27 seconds wall clock time: 46 minutes 23.49 seconds (2783.49 seconds total)