Starting phenix.real_space_refine on Thu Jul 24 22:34:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sqf_25383/07_2025/7sqf_25383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sqf_25383/07_2025/7sqf_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_25383/07_2025/7sqf_25383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sqf_25383/07_2025/7sqf_25383.map" model { file = "/net/cci-nas-00/data/ceres_data/7sqf_25383/07_2025/7sqf_25383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sqf_25383/07_2025/7sqf_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-5711/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: 4.59, per 1000 atoms: 0.69 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: 1.66 Conformation dependent library (CDL) restraints added in 912.6 milliseconds 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: 0.47 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: 1.49 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 2.310 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.450 Find NCS groups from input model: 0.120 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.430 ------------------------------------------------------------------------------- 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 6807 Z= 0.249 Angle : 0.663 9.545 9264 Z= 0.354 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00676 ( 12) link_NAG-ASN : angle 4.49953 ( 36) hydrogen bonds : bond 0.12086 ( 225) hydrogen bonds : angle 4.83171 ( 657) covalent geometry : bond 0.00455 ( 6795) covalent geometry : angle 0.60243 ( 9228) *********************** 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 : 0.680 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: 0.3088 time to fit residues: 97.8789 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 : 0.804 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.120329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106984 restraints weight = 12746.564| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.91 r_work: 0.3375 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 6807 Z= 0.241 Angle : 0.636 10.611 9264 Z= 0.319 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00837 ( 12) link_NAG-ASN : angle 3.85956 ( 36) hydrogen bonds : bond 0.03299 ( 225) hydrogen bonds : angle 4.18670 ( 657) covalent geometry : bond 0.00551 ( 6795) covalent geometry : angle 0.59016 ( 9228) *********************** 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 : 0.795 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: 0.8036 (mt) cc_final: 0.7812 (mm) REVERT: A 93 ARG cc_start: 0.8590 (ttt180) cc_final: 0.8228 (ttt180) REVERT: A 94 GLU cc_start: 0.7965 (mp0) cc_final: 0.7142 (mp0) REVERT: A 101 MET cc_start: 0.9095 (mtt) cc_final: 0.8891 (mtt) REVERT: A 106 LYS cc_start: 0.8194 (ttpt) cc_final: 0.7866 (ptmt) REVERT: A 133 GLU cc_start: 0.7704 (tp30) cc_final: 0.7387 (tp30) REVERT: A 143 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8396 (mm-40) REVERT: A 147 MET cc_start: 0.8424 (ttm) cc_final: 0.8197 (ttm) REVERT: A 175 ARG cc_start: 0.7562 (ttt90) cc_final: 0.7286 (ttt90) REVERT: A 179 LYS cc_start: 0.8330 (tptt) cc_final: 0.7829 (tptt) REVERT: A 200 ASP cc_start: 0.8272 (m-30) cc_final: 0.7983 (m-30) REVERT: A 208 GLN cc_start: 0.8045 (tp40) cc_final: 0.7841 (tp-100) REVERT: A 224 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 294 LYS cc_start: 0.8928 (mttp) cc_final: 0.8633 (mttm) REVERT: A 306 THR cc_start: 0.7611 (m) cc_final: 0.7199 (p) REVERT: A 314 PHE cc_start: 0.8188 (t80) cc_final: 0.7981 (t80) REVERT: B 92 PHE cc_start: 0.8697 (t80) cc_final: 0.8366 (t80) REVERT: B 94 GLU cc_start: 0.8088 (mp0) cc_final: 0.7229 (mp0) REVERT: B 96 LEU cc_start: 0.9175 (mt) cc_final: 0.8880 (mt) REVERT: B 106 LYS cc_start: 0.8161 (ttpt) cc_final: 0.7789 (ptmt) REVERT: B 166 LYS cc_start: 0.8340 (mtpt) cc_final: 0.8137 (mtpp) REVERT: B 188 ARG cc_start: 0.8898 (tmm-80) cc_final: 0.8601 (ttt-90) REVERT: B 224 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7814 (mt-10) REVERT: B 297 ASP cc_start: 0.7924 (p0) cc_final: 0.7715 (p0) REVERT: B 306 THR cc_start: 0.7734 (m) cc_final: 0.7269 (p) REVERT: C 71 ILE cc_start: 0.8278 (mt) cc_final: 0.7999 (mp) REVERT: C 75 LEU cc_start: 0.7995 (mt) cc_final: 0.7731 (mt) REVERT: C 87 ARG cc_start: 0.7743 (tpt-90) cc_final: 0.7436 (tpt-90) REVERT: C 96 LEU cc_start: 0.9121 (mt) cc_final: 0.8815 (mp) REVERT: C 106 LYS cc_start: 0.8167 (ttpt) cc_final: 0.7716 (ttpp) REVERT: C 124 GLN cc_start: 0.8444 (tt0) cc_final: 0.8186 (pt0) REVERT: C 143 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8396 (mm110) REVERT: C 243 SER cc_start: 0.8960 (m) cc_final: 0.8541 (p) REVERT: C 260 GLN cc_start: 0.8217 (pt0) cc_final: 0.7832 (pt0) REVERT: C 269 ASP cc_start: 0.8757 (p0) cc_final: 0.8557 (p0) REVERT: C 297 ASP cc_start: 0.7689 (p0) cc_final: 0.7264 (p0) REVERT: C 314 PHE cc_start: 0.8128 (t80) cc_final: 0.7818 (t80) outliers start: 8 outliers final: 4 residues processed: 261 average time/residue: 0.2934 time to fit residues: 92.1262 Evaluate side-chains 259 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 254 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain C residue 143 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3692 r_free = 0.3692 target = 0.117806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.104619 restraints weight = 12794.799| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.90 r_work: 0.3337 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 6807 Z= 0.250 Angle : 0.600 9.027 9264 Z= 0.308 Chirality : 0.048 0.338 1062 Planarity : 0.004 0.029 1158 Dihedral : 5.467 56.022 1134 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.54 % Allowed : 13.57 % Favored : 82.89 % 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: 2.74 (0.29), residues: 282 sheet: 0.29 (0.29), residues: 315 loop : -0.92 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.004 0.002 HIS C 98 PHE 0.019 0.002 PHE B 314 TYR 0.013 0.002 TYR B 119 ARG 0.004 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00851 ( 12) link_NAG-ASN : angle 3.76358 ( 36) hydrogen bonds : bond 0.03472 ( 225) hydrogen bonds : angle 4.10140 ( 657) covalent geometry : bond 0.00570 ( 6795) covalent geometry : angle 0.55314 ( 9228) *********************** 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 276 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 252 time to evaluate : 0.693 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: 0.8536 (m) cc_final: 0.7222 (p) REVERT: A 93 ARG cc_start: 0.8662 (ttt180) cc_final: 0.8297 (ttt180) REVERT: A 94 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: A 106 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7879 (tptp) REVERT: A 133 GLU cc_start: 0.7678 (tp30) cc_final: 0.7390 (tp30) REVERT: A 143 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8533 (mm110) REVERT: A 146 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.7211 (t70) REVERT: A 166 LYS cc_start: 0.8526 (mtpp) cc_final: 0.8124 (mtpt) REVERT: A 209 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7106 (pt0) REVERT: A 224 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7921 (mt-10) REVERT: A 279 GLN cc_start: 0.8394 (mt0) cc_final: 0.8179 (mt0) REVERT: A 306 THR cc_start: 0.7653 (m) cc_final: 0.7254 (p) REVERT: A 314 PHE cc_start: 0.8160 (t80) cc_final: 0.7940 (t80) REVERT: B 92 PHE cc_start: 0.8776 (t80) cc_final: 0.8483 (t80) REVERT: B 95 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8694 (mtmm) REVERT: B 96 LEU cc_start: 0.9196 (mt) cc_final: 0.8880 (mt) REVERT: B 106 LYS cc_start: 0.8155 (ttpt) cc_final: 0.7859 (ptmt) REVERT: B 224 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7817 (mt-10) REVERT: B 306 THR cc_start: 0.7693 (m) cc_final: 0.7341 (p) REVERT: C 75 LEU cc_start: 0.8130 (mt) cc_final: 0.7838 (mm) REVERT: C 80 VAL cc_start: 0.8422 (t) cc_final: 0.8166 (p) REVERT: C 87 ARG cc_start: 0.7889 (tpt-90) cc_final: 0.7632 (tpt-90) REVERT: C 96 LEU cc_start: 0.9140 (mt) cc_final: 0.8867 (mp) REVERT: C 143 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8367 (mm110) REVERT: C 224 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7909 (mt-10) REVERT: C 243 SER cc_start: 0.8913 (m) cc_final: 0.8418 (p) REVERT: C 297 ASP cc_start: 0.7621 (p0) cc_final: 0.6984 (p0) REVERT: C 314 PHE cc_start: 0.8098 (t80) cc_final: 0.7792 (t80) outliers start: 24 outliers final: 14 residues processed: 260 average time/residue: 0.2826 time to fit residues: 87.7672 Evaluate side-chains 254 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 235 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 146 ASP Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 209 GLU 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 151 THR 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 143 GLN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 72 optimal weight: 0.5980 chunk 13 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 172 GLN C 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.119208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.106038 restraints weight = 12909.321| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.92 r_work: 0.3357 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6807 Z= 0.177 Angle : 0.543 8.874 9264 Z= 0.278 Chirality : 0.045 0.333 1062 Planarity : 0.003 0.024 1158 Dihedral : 4.808 45.803 1134 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % 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: 1.26 (0.30), residues: 813 helix: 2.82 (0.29), residues: 282 sheet: 0.22 (0.30), residues: 315 loop : -0.87 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.003 0.001 HIS A 130 PHE 0.016 0.002 PHE A 232 TYR 0.015 0.001 TYR B 227 ARG 0.005 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00794 ( 12) link_NAG-ASN : angle 3.60791 ( 36) hydrogen bonds : bond 0.03192 ( 225) hydrogen bonds : angle 3.89722 ( 657) covalent geometry : bond 0.00409 ( 6795) covalent geometry : angle 0.49490 ( 9228) *********************** 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 262 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.742 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: 0.8581 (m) cc_final: 0.8254 (p) REVERT: A 92 PHE cc_start: 0.8789 (t80) cc_final: 0.8508 (t80) REVERT: A 93 ARG cc_start: 0.8725 (ttt180) cc_final: 0.8357 (ttt180) REVERT: A 106 LYS cc_start: 0.8193 (ttpt) cc_final: 0.7849 (tptp) REVERT: A 133 GLU cc_start: 0.7624 (tp30) cc_final: 0.7348 (tp30) REVERT: A 143 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8430 (mm-40) REVERT: A 166 LYS cc_start: 0.8469 (mtpp) cc_final: 0.8016 (mtpt) REVERT: A 209 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.7043 (pt0) REVERT: A 224 GLU cc_start: 0.8337 (mm-30) cc_final: 0.7910 (mt-10) REVERT: A 231 LYS cc_start: 0.8896 (mttm) cc_final: 0.8579 (mttm) REVERT: A 306 THR cc_start: 0.7623 (m) cc_final: 0.7233 (p) REVERT: A 314 PHE cc_start: 0.8190 (t80) cc_final: 0.7972 (t80) REVERT: B 92 PHE cc_start: 0.8799 (t80) cc_final: 0.8511 (t80) REVERT: B 96 LEU cc_start: 0.9167 (mt) cc_final: 0.8872 (mt) REVERT: B 106 LYS cc_start: 0.8203 (ttpt) cc_final: 0.7872 (ptmt) REVERT: B 146 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.7182 (t70) REVERT: B 224 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7862 (mt-10) REVERT: B 306 THR cc_start: 0.7660 (m) cc_final: 0.7326 (p) REVERT: C 75 LEU cc_start: 0.8138 (mt) cc_final: 0.7859 (mm) REVERT: C 80 VAL cc_start: 0.8422 (t) cc_final: 0.8147 (p) REVERT: C 87 ARG cc_start: 0.7885 (tpt-90) cc_final: 0.7555 (tpt-90) REVERT: C 94 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: C 143 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8306 (mm-40) REVERT: C 176 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7721 (mt-10) REVERT: C 224 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7909 (mt-10) REVERT: C 243 SER cc_start: 0.8879 (m) cc_final: 0.8367 (p) REVERT: C 297 ASP cc_start: 0.7602 (p0) cc_final: 0.6957 (p0) REVERT: C 314 PHE cc_start: 0.8086 (t80) cc_final: 0.7761 (t80) outliers start: 21 outliers final: 12 residues processed: 246 average time/residue: 0.3195 time to fit residues: 93.3166 Evaluate side-chains 255 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 238 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 157 THR Chi-restraints excluded: chain A residue 209 GLU 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 146 ASP Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU Chi-restraints excluded: chain C residue 143 GLN Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 241 LYS Chi-restraints excluded: chain C residue 242 MET Chi-restraints excluded: chain C residue 279 GLN 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 47 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 23 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 63 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 29 optimal weight: 0.0270 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.122795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.109886 restraints weight = 12738.147| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.87 r_work: 0.3396 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6807 Z= 0.124 Angle : 0.563 10.178 9264 Z= 0.279 Chirality : 0.047 0.387 1062 Planarity : 0.003 0.023 1158 Dihedral : 5.312 49.009 1134 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.54 % Allowed : 20.94 % Favored : 75.52 % 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: 1.32 (0.30), residues: 813 helix: 2.90 (0.29), residues: 282 sheet: 0.19 (0.30), residues: 315 loop : -0.76 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.006 0.001 HIS B 130 PHE 0.014 0.001 PHE B 318 TYR 0.009 0.001 TYR A 201 ARG 0.004 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 12) link_NAG-ASN : angle 3.91329 ( 36) hydrogen bonds : bond 0.02973 ( 225) hydrogen bonds : angle 3.69793 ( 657) covalent geometry : bond 0.00288 ( 6795) covalent geometry : angle 0.50797 ( 9228) *********************** 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 261 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 237 time to evaluate : 0.733 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 90 THR cc_start: 0.8559 (m) cc_final: 0.8209 (p) REVERT: A 92 PHE cc_start: 0.8779 (t80) cc_final: 0.8495 (t80) REVERT: A 93 ARG cc_start: 0.8686 (ttt180) cc_final: 0.8301 (ttt180) REVERT: A 106 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7856 (tptp) REVERT: A 129 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8438 (mtpp) REVERT: A 133 GLU cc_start: 0.7653 (tp30) cc_final: 0.7402 (tp30) REVERT: A 143 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8509 (mm110) REVERT: A 146 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.7023 (t70) REVERT: A 166 LYS cc_start: 0.8437 (mtpp) cc_final: 0.8003 (mtpt) REVERT: A 224 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7909 (mt-10) REVERT: A 231 LYS cc_start: 0.8807 (mttm) cc_final: 0.8559 (mttp) REVERT: A 279 GLN cc_start: 0.8354 (mt0) cc_final: 0.8107 (mt0) REVERT: A 314 PHE cc_start: 0.8198 (t80) cc_final: 0.7966 (t80) REVERT: B 92 PHE cc_start: 0.8790 (t80) cc_final: 0.8562 (t80) REVERT: B 94 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7212 (mp0) REVERT: B 96 LEU cc_start: 0.9153 (mt) cc_final: 0.8858 (mt) REVERT: B 106 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7892 (ptmt) REVERT: B 143 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8228 (mm-40) REVERT: B 146 ASP cc_start: 0.7490 (OUTLIER) cc_final: 0.7167 (t70) REVERT: B 224 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7950 (mt-10) REVERT: B 306 THR cc_start: 0.7652 (m) cc_final: 0.7269 (p) REVERT: C 75 LEU cc_start: 0.8108 (mt) cc_final: 0.7835 (mm) REVERT: C 80 VAL cc_start: 0.8404 (t) cc_final: 0.8132 (p) REVERT: C 87 ARG cc_start: 0.7859 (tpt-90) cc_final: 0.7535 (tpt-90) REVERT: C 94 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7213 (mp0) REVERT: C 143 GLN cc_start: 0.8631 (mm110) cc_final: 0.8339 (mm110) REVERT: C 224 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7943 (mt-10) REVERT: C 297 ASP cc_start: 0.7625 (p0) cc_final: 0.6913 (p0) REVERT: C 314 PHE cc_start: 0.8053 (t80) cc_final: 0.7721 (t80) outliers start: 24 outliers final: 11 residues processed: 244 average time/residue: 0.2981 time to fit residues: 86.6877 Evaluate side-chains 258 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 243 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 146 ASP 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 135 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 242 MET Chi-restraints excluded: chain C residue 94 GLU 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 59 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 72 optimal weight: 0.5980 chunk 62 optimal weight: 0.0060 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 130 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.119883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107034 restraints weight = 12767.702| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 2.89 r_work: 0.3388 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6807 Z= 0.159 Angle : 0.545 8.774 9264 Z= 0.279 Chirality : 0.046 0.331 1062 Planarity : 0.003 0.022 1158 Dihedral : 5.046 58.572 1134 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.98 % Allowed : 20.50 % Favored : 75.52 % 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: 1.23 (0.30), residues: 813 helix: 2.82 (0.29), residues: 282 sheet: 0.12 (0.30), residues: 315 loop : -0.75 (0.43), residues: 216 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 0.015 0.001 PHE A 232 TYR 0.008 0.001 TYR A 201 ARG 0.003 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00866 ( 12) link_NAG-ASN : angle 3.57853 ( 36) hydrogen bonds : bond 0.03197 ( 225) hydrogen bonds : angle 3.78286 ( 657) covalent geometry : bond 0.00371 ( 6795) covalent geometry : angle 0.49867 ( 9228) *********************** 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 271 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.689 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 92 PHE cc_start: 0.8764 (t80) cc_final: 0.8464 (t80) REVERT: A 93 ARG cc_start: 0.8767 (ttt180) cc_final: 0.8404 (ttt180) REVERT: A 106 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7855 (tptp) REVERT: A 129 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8407 (mtpp) REVERT: A 133 GLU cc_start: 0.7594 (tp30) cc_final: 0.7364 (tp30) REVERT: A 146 ASP cc_start: 0.7357 (OUTLIER) cc_final: 0.7108 (t70) REVERT: A 175 ARG cc_start: 0.7424 (ttt90) cc_final: 0.6717 (tpt90) REVERT: A 209 GLU cc_start: 0.7255 (pt0) cc_final: 0.6896 (pt0) REVERT: A 224 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7930 (mt-10) REVERT: A 231 LYS cc_start: 0.8852 (mttm) cc_final: 0.8616 (mttp) REVERT: A 279 GLN cc_start: 0.8393 (mt0) cc_final: 0.8151 (mt0) REVERT: A 289 ASP cc_start: 0.8039 (p0) cc_final: 0.7833 (p0) REVERT: A 314 PHE cc_start: 0.8187 (t80) cc_final: 0.7972 (t80) REVERT: B 92 PHE cc_start: 0.8780 (t80) cc_final: 0.8552 (t80) REVERT: B 94 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: B 96 LEU cc_start: 0.9161 (mt) cc_final: 0.8858 (mt) REVERT: B 106 LYS cc_start: 0.8182 (ttpt) cc_final: 0.7851 (ptmt) REVERT: B 146 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7094 (t70) REVERT: B 224 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7930 (mt-10) REVERT: B 306 THR cc_start: 0.7706 (m) cc_final: 0.7358 (p) REVERT: C 75 LEU cc_start: 0.8194 (mt) cc_final: 0.7942 (mm) REVERT: C 80 VAL cc_start: 0.8422 (t) cc_final: 0.8155 (p) REVERT: C 94 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7239 (mp0) REVERT: C 143 GLN cc_start: 0.8652 (mm110) cc_final: 0.8377 (mm110) REVERT: C 297 ASP cc_start: 0.7627 (p0) cc_final: 0.6937 (p0) REVERT: C 314 PHE cc_start: 0.8125 (t80) cc_final: 0.7793 (t80) outliers start: 27 outliers final: 16 residues processed: 252 average time/residue: 0.2968 time to fit residues: 88.9674 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 : 0.910 ------------------------------------------------------------------------------- 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 146 ASP 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 146 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 224 GLU 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 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 45 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 36 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.2980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS B 98 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.121591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.108445 restraints weight = 12685.203| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 2.91 r_work: 0.3401 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6807 Z= 0.133 Angle : 0.585 13.860 9264 Z= 0.290 Chirality : 0.048 0.459 1062 Planarity : 0.003 0.023 1158 Dihedral : 5.450 47.118 1134 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.54 % Allowed : 22.27 % Favored : 74.19 % 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: 1.22 (0.30), residues: 813 helix: 2.81 (0.29), residues: 282 sheet: 0.05 (0.29), residues: 315 loop : -0.64 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 230 HIS 0.004 0.001 HIS B 98 PHE 0.025 0.001 PHE A 83 TYR 0.008 0.001 TYR A 201 ARG 0.005 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 12) link_NAG-ASN : angle 4.19125 ( 36) hydrogen bonds : bond 0.03141 ( 225) hydrogen bonds : angle 3.70257 ( 657) covalent geometry : bond 0.00311 ( 6795) covalent geometry : angle 0.52413 ( 9228) *********************** 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 266 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 242 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 THR cc_start: 0.8507 (m) cc_final: 0.8261 (p) REVERT: A 92 PHE cc_start: 0.8754 (t80) cc_final: 0.8453 (t80) REVERT: A 93 ARG cc_start: 0.8776 (ttt180) cc_final: 0.8402 (ttt180) REVERT: A 106 LYS cc_start: 0.8214 (ttpt) cc_final: 0.7864 (tptp) REVERT: A 129 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8454 (mtpp) REVERT: A 133 GLU cc_start: 0.7564 (tp30) cc_final: 0.7333 (tp30) REVERT: A 146 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6975 (t70) REVERT: A 175 ARG cc_start: 0.7420 (ttt90) cc_final: 0.6689 (tpt90) REVERT: A 209 GLU cc_start: 0.7259 (pt0) cc_final: 0.6914 (pt0) REVERT: A 224 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7968 (mt-10) REVERT: A 231 LYS cc_start: 0.8837 (mttm) cc_final: 0.8623 (mttp) REVERT: A 279 GLN cc_start: 0.8369 (mt0) cc_final: 0.8118 (mt0) REVERT: A 289 ASP cc_start: 0.7992 (p0) cc_final: 0.7755 (p0) REVERT: A 314 PHE cc_start: 0.8165 (t80) cc_final: 0.7948 (t80) REVERT: B 92 PHE cc_start: 0.8773 (t80) cc_final: 0.8565 (t80) REVERT: B 94 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: B 96 LEU cc_start: 0.9150 (mt) cc_final: 0.8850 (mt) REVERT: B 106 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7875 (ptmt) REVERT: B 146 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7033 (t70) REVERT: B 224 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: B 306 THR cc_start: 0.7631 (m) cc_final: 0.7258 (p) REVERT: C 75 LEU cc_start: 0.8181 (mt) cc_final: 0.7938 (mm) REVERT: C 80 VAL cc_start: 0.8432 (t) cc_final: 0.8169 (p) REVERT: C 94 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: C 133 GLU cc_start: 0.7686 (tp30) cc_final: 0.7357 (mp0) REVERT: C 143 GLN cc_start: 0.8632 (mm110) cc_final: 0.8353 (mm110) REVERT: C 224 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7956 (mt-10) REVERT: C 297 ASP cc_start: 0.7596 (p0) cc_final: 0.6901 (p0) REVERT: C 314 PHE cc_start: 0.8095 (t80) cc_final: 0.7761 (t80) outliers start: 24 outliers final: 17 residues processed: 250 average time/residue: 0.2901 time to fit residues: 86.3369 Evaluate side-chains 262 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ASP 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 124 GLN Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 GLU Chi-restraints excluded: chain B residue 224 GLU 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 242 MET 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 37 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 65 optimal weight: 0.4980 chunk 30 optimal weight: 0.0870 chunk 18 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 32 optimal weight: 0.0050 chunk 57 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.3572 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.126916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.113601 restraints weight = 12685.565| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.85 r_work: 0.3427 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6807 Z= 0.131 Angle : 0.551 8.722 9264 Z= 0.279 Chirality : 0.046 0.344 1062 Planarity : 0.003 0.028 1158 Dihedral : 4.986 51.991 1134 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.83 % Allowed : 21.68 % Favored : 74.48 % 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: 1.19 (0.30), residues: 813 helix: 2.78 (0.29), residues: 282 sheet: -0.02 (0.29), residues: 318 loop : -0.57 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 230 HIS 0.003 0.001 HIS A 130 PHE 0.014 0.001 PHE B 318 TYR 0.008 0.001 TYR A 201 ARG 0.008 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00882 ( 12) link_NAG-ASN : angle 3.59001 ( 36) hydrogen bonds : bond 0.03122 ( 225) hydrogen bonds : angle 3.69700 ( 657) covalent geometry : bond 0.00307 ( 6795) covalent geometry : angle 0.50405 ( 9228) *********************** 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 269 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 243 time to evaluate : 0.781 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 90 THR cc_start: 0.8514 (m) cc_final: 0.8277 (p) REVERT: A 92 PHE cc_start: 0.8710 (t80) cc_final: 0.8406 (t80) REVERT: A 93 ARG cc_start: 0.8847 (ttt180) cc_final: 0.8501 (ttt180) REVERT: A 106 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7839 (tptp) REVERT: A 129 LYS cc_start: 0.8788 (mmmt) cc_final: 0.8342 (mtpp) REVERT: A 133 GLU cc_start: 0.7511 (tp30) cc_final: 0.7304 (tp30) REVERT: A 146 ASP cc_start: 0.7130 (OUTLIER) cc_final: 0.6803 (t70) REVERT: A 166 LYS cc_start: 0.8265 (mtpp) cc_final: 0.8061 (mtpt) REVERT: A 209 GLU cc_start: 0.7192 (pt0) cc_final: 0.6870 (pt0) REVERT: A 279 GLN cc_start: 0.8377 (mt0) cc_final: 0.8141 (mt0) REVERT: A 289 ASP cc_start: 0.7928 (p0) cc_final: 0.7677 (p0) REVERT: A 306 THR cc_start: 0.7581 (m) cc_final: 0.7214 (p) REVERT: A 314 PHE cc_start: 0.8117 (t80) cc_final: 0.7912 (t80) REVERT: B 94 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: B 97 LYS cc_start: 0.8590 (ttmt) cc_final: 0.8370 (ttmt) REVERT: B 106 LYS cc_start: 0.8117 (ttpt) cc_final: 0.7814 (ptmt) REVERT: B 146 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6918 (t0) REVERT: C 75 LEU cc_start: 0.8208 (mt) cc_final: 0.7999 (mm) REVERT: C 80 VAL cc_start: 0.8446 (t) cc_final: 0.8184 (p) REVERT: C 94 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: C 133 GLU cc_start: 0.7616 (tp30) cc_final: 0.7329 (mp0) REVERT: C 143 GLN cc_start: 0.8661 (mm110) cc_final: 0.8389 (mm110) REVERT: C 175 ARG cc_start: 0.7548 (ttt90) cc_final: 0.7344 (tpt90) REVERT: C 179 LYS cc_start: 0.8342 (mttp) cc_final: 0.7996 (mttp) REVERT: C 224 GLU cc_start: 0.8335 (mm-30) cc_final: 0.8003 (mt-10) REVERT: C 297 ASP cc_start: 0.7618 (p0) cc_final: 0.6936 (p0) REVERT: C 314 PHE cc_start: 0.8040 (t80) cc_final: 0.7714 (t80) outliers start: 26 outliers final: 16 residues processed: 251 average time/residue: 0.3041 time to fit residues: 90.4718 Evaluate side-chains 258 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ASP 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 98 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 GLU 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 279 GLN 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 26 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 34 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 HIS B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.121074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107591 restraints weight = 12642.272| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.87 r_work: 0.3398 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6807 Z= 0.191 Angle : 0.580 8.744 9264 Z= 0.302 Chirality : 0.046 0.330 1062 Planarity : 0.003 0.031 1158 Dihedral : 5.170 57.016 1134 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.39 % Allowed : 22.71 % Favored : 73.89 % 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: 2.63 (0.29), residues: 282 sheet: -0.07 (0.29), residues: 318 loop : -0.63 (0.43), residues: 213 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 0.026 0.002 PHE C 323 TYR 0.010 0.001 TYR B 119 ARG 0.008 0.000 ARG C 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00855 ( 12) link_NAG-ASN : angle 3.44217 ( 36) hydrogen bonds : bond 0.03469 ( 225) hydrogen bonds : angle 3.99026 ( 657) covalent geometry : bond 0.00447 ( 6795) covalent geometry : angle 0.53937 ( 9228) *********************** 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 262 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.688 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: 0.8554 (m) cc_final: 0.8285 (p) REVERT: A 92 PHE cc_start: 0.8723 (t80) cc_final: 0.8457 (t80) REVERT: A 93 ARG cc_start: 0.8846 (ttt180) cc_final: 0.8501 (ttt180) REVERT: A 106 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7841 (tptp) REVERT: A 129 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8323 (mtpp) REVERT: A 133 GLU cc_start: 0.7518 (tp30) cc_final: 0.7308 (tp30) REVERT: A 146 ASP cc_start: 0.7242 (OUTLIER) cc_final: 0.6850 (t70) REVERT: A 209 GLU cc_start: 0.7271 (pt0) cc_final: 0.6960 (pt0) REVERT: A 279 GLN cc_start: 0.8409 (mt0) cc_final: 0.8183 (mt0) REVERT: A 289 ASP cc_start: 0.7997 (p0) cc_final: 0.7746 (p0) REVERT: B 93 ARG cc_start: 0.8679 (ttt180) cc_final: 0.8465 (ttt90) REVERT: B 94 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: B 106 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7776 (ptmt) REVERT: B 146 ASP cc_start: 0.7254 (OUTLIER) cc_final: 0.6917 (t0) REVERT: B 306 THR cc_start: 0.7727 (m) cc_final: 0.7397 (p) REVERT: C 75 LEU cc_start: 0.8279 (mt) cc_final: 0.8070 (mm) REVERT: C 80 VAL cc_start: 0.8466 (t) cc_final: 0.8205 (p) REVERT: C 94 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: C 143 GLN cc_start: 0.8648 (mm110) cc_final: 0.8332 (mm-40) REVERT: C 224 GLU cc_start: 0.8347 (mm-30) cc_final: 0.7927 (mt-10) REVERT: C 243 SER cc_start: 0.8896 (m) cc_final: 0.8416 (p) REVERT: C 297 ASP cc_start: 0.7625 (p0) cc_final: 0.6981 (p0) REVERT: C 314 PHE cc_start: 0.8085 (t80) cc_final: 0.7779 (t80) outliers start: 23 outliers final: 18 residues processed: 246 average time/residue: 0.2988 time to fit residues: 87.4754 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 : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 146 ASP 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 95 LYS Chi-restraints excluded: chain B residue 98 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 GLU 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 166 LYS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET 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 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS B 98 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.120648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.107235 restraints weight = 12834.266| |-----------------------------------------------------------------------------| r_work (start): 0.3544 rms_B_bonded: 2.88 r_work: 0.3398 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6807 Z= 0.192 Angle : 0.584 8.753 9264 Z= 0.307 Chirality : 0.046 0.331 1062 Planarity : 0.003 0.027 1158 Dihedral : 5.064 49.322 1134 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.54 % Allowed : 23.30 % Favored : 73.16 % 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: 0.93 (0.30), residues: 813 helix: 2.52 (0.28), residues: 282 sheet: -0.18 (0.29), residues: 318 loop : -0.59 (0.43), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 230 HIS 0.008 0.001 HIS B 98 PHE 0.026 0.002 PHE A 314 TYR 0.009 0.001 TYR B 227 ARG 0.002 0.000 ARG B 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00849 ( 12) link_NAG-ASN : angle 3.39504 ( 36) hydrogen bonds : bond 0.03563 ( 225) hydrogen bonds : angle 3.97920 ( 657) covalent geometry : bond 0.00448 ( 6795) covalent geometry : angle 0.54574 ( 9228) ********************** 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 270 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 0.693 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: 0.8565 (m) cc_final: 0.8296 (p) REVERT: A 93 ARG cc_start: 0.8814 (ttt180) cc_final: 0.8461 (ttt180) REVERT: A 106 LYS cc_start: 0.8133 (ttpt) cc_final: 0.7857 (tptp) REVERT: A 129 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8347 (mtpp) REVERT: A 133 GLU cc_start: 0.7521 (tp30) cc_final: 0.7315 (tp30) REVERT: A 146 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6840 (t70) REVERT: A 175 ARG cc_start: 0.7273 (mmm160) cc_final: 0.7018 (tpt90) REVERT: A 209 GLU cc_start: 0.7265 (pt0) cc_final: 0.6937 (pt0) REVERT: A 279 GLN cc_start: 0.8378 (mt0) cc_final: 0.8147 (mt0) REVERT: A 289 ASP cc_start: 0.8022 (p0) cc_final: 0.7746 (p0) REVERT: B 106 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7794 (ptmt) REVERT: B 146 ASP cc_start: 0.7237 (OUTLIER) cc_final: 0.6898 (t70) REVERT: B 306 THR cc_start: 0.7694 (m) cc_final: 0.7375 (p) REVERT: C 75 LEU cc_start: 0.8271 (mt) cc_final: 0.8070 (mm) REVERT: C 80 VAL cc_start: 0.8466 (t) cc_final: 0.8203 (p) REVERT: C 87 ARG cc_start: 0.7936 (tpt-90) cc_final: 0.7719 (tpt-90) REVERT: C 94 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: C 133 GLU cc_start: 0.7677 (tp30) cc_final: 0.7351 (mp0) REVERT: C 143 GLN cc_start: 0.8646 (mm110) cc_final: 0.8377 (mm110) REVERT: C 224 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7911 (mt-10) REVERT: C 231 LYS cc_start: 0.9011 (mttp) cc_final: 0.8783 (mttm) REVERT: C 297 ASP cc_start: 0.7633 (p0) cc_final: 0.6990 (p0) REVERT: C 314 PHE cc_start: 0.8097 (t80) cc_final: 0.7809 (t80) outliers start: 24 outliers final: 20 residues processed: 253 average time/residue: 0.2852 time to fit residues: 86.0828 Evaluate side-chains 271 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 98 HIS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 146 ASP 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 98 HIS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 146 ASP Chi-restraints excluded: chain B residue 166 LYS Chi-restraints excluded: chain B residue 176 GLU 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 166 LYS Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 242 MET 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 46 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 61 optimal weight: 0.0270 chunk 64 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 0.0970 chunk 21 optimal weight: 0.1980 chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 2 optimal weight: 0.0770 chunk 50 optimal weight: 0.2980 overall best weight: 0.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS B 98 HIS B 266 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.124358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.110872 restraints weight = 12775.495| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.90 r_work: 0.3457 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6807 Z= 0.107 Angle : 0.551 8.701 9264 Z= 0.284 Chirality : 0.046 0.329 1062 Planarity : 0.003 0.027 1158 Dihedral : 4.731 44.558 1134 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.36 % Allowed : 25.07 % Favored : 72.57 % 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: 2.62 (0.28), residues: 282 sheet: -0.17 (0.29), residues: 318 loop : -0.41 (0.44), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 230 HIS 0.009 0.001 HIS B 98 PHE 0.029 0.001 PHE A 314 TYR 0.009 0.001 TYR A 201 ARG 0.001 0.000 ARG C 87 Details of bonding type rmsd link_NAG-ASN : bond 0.00819 ( 12) link_NAG-ASN : angle 3.32799 ( 36) hydrogen bonds : bond 0.03228 ( 225) hydrogen bonds : angle 3.73667 ( 657) covalent geometry : bond 0.00246 ( 6795) covalent geometry : angle 0.51173 ( 9228) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3773.63 seconds wall clock time: 65 minutes 37.12 seconds (3937.12 seconds total)