Starting phenix.real_space_refine on Wed Jul 1 23:29:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dls_27514/07_2026/8dls_27514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dls_27514/07_2026/8dls_27514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2026/8dls_27514.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2026/8dls_27514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2026/8dls_27514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2026/8dls_27514.map" model { file = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2026/8dls_27514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dls_27514/07_2026/8dls_27514.cif" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.016 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 18 5.16 5 C 2566 2.51 5 N 648 2.21 5 O 785 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4017 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2081 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 12, 'TRANS': 242} Chain breaks: 3 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.12, per 1000 atoms: 0.28 Number of scatterers: 4017 At special positions: 0 Unit cell: (95, 61, 101, 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 18 16.00 O 785 8.00 N 648 7.00 C 2566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 149 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 143.6 milliseconds 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 10 sheets defined 2.6% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 3.910A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing helix chain 'L' and resid 104 through 108 removed outlier: 3.963A pdb=" N VAL L 108 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 8.072A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.764A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.606A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.627A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.225A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.813A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.170A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.959A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31 removed outlier: 6.164A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR H 141 " --> pdb=" O TYR H 113 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 3.758A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 144 hydrogen bonds defined for protein. 357 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.59 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1235 1.34 - 1.46: 1022 1.46 - 1.58: 1834 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 4118 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.463 -0.057 2.00e-02 2.50e+03 8.24e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.90e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C ARG A 102 " pdb=" N GLY A 103 " ideal model delta sigma weight residual 1.327 1.307 0.020 1.11e-02 8.12e+03 3.25e+00 ... (remaining 4113 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 5450 2.47 - 4.95: 130 4.95 - 7.42: 14 7.42 - 9.90: 1 9.90 - 12.37: 2 Bond angle restraints: 5597 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 132.21 -10.67 1.91e+00 2.74e-01 3.12e+01 angle pdb=" CA LEU H 127 " pdb=" CB LEU H 127 " pdb=" CG LEU H 127 " ideal model delta sigma weight residual 116.30 128.67 -12.37 3.50e+00 8.16e-02 1.25e+01 angle pdb=" C GLN H 139 " pdb=" N GLY H 140 " pdb=" CA GLY H 140 " ideal model delta sigma weight residual 122.73 119.73 3.00 9.30e-01 1.16e+00 1.04e+01 angle pdb=" CA THR L 56 " pdb=" CB THR L 56 " pdb=" CG2 THR L 56 " ideal model delta sigma weight residual 110.50 115.81 -5.31 1.70e+00 3.46e-01 9.77e+00 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 115.70 -3.10 1.00e+00 1.00e+00 9.64e+00 ... (remaining 5592 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.40: 2190 17.40 - 34.79: 137 34.79 - 52.18: 21 52.18 - 69.57: 4 69.57 - 86.97: 5 Dihedral angle restraints: 2357 sinusoidal: 919 harmonic: 1438 Sorted by residual: dihedral pdb=" CA ASN A 149 " pdb=" C ASN A 149 " pdb=" N LYS A 150 " pdb=" CA LYS A 150 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA LYS H 31 " pdb=" C LYS H 31 " pdb=" N LYS H 32 " pdb=" CA LYS H 32 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ILE A 128 " pdb=" C ILE A 128 " pdb=" N LYS A 129 " pdb=" CA LYS A 129 " ideal model delta harmonic sigma weight residual 180.00 -159.53 -20.47 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 2354 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 572 0.097 - 0.193: 57 0.193 - 0.290: 3 0.290 - 0.386: 0 0.386 - 0.483: 3 Chirality restraints: 635 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 149 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" CB THR L 56 " pdb=" CA THR L 56 " pdb=" OG1 THR L 56 " pdb=" CG2 THR L 56 " both_signs ideal model delta sigma weight residual False 2.55 2.14 0.41 2.00e-01 2.50e+01 4.19e+00 ... (remaining 632 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 149 " 0.005 2.00e-02 2.50e+03 2.66e-02 8.87e+00 pdb=" CG ASN A 149 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 149 " 0.031 2.00e-02 2.50e+03 pdb=" ND2 ASN A 149 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG A1302 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 198 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" CG ASP A 198 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP A 198 " -0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 198 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 83 " 0.042 5.00e-02 4.00e+02 6.39e-02 6.53e+00 pdb=" N PRO L 84 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO L 84 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 84 " 0.035 5.00e-02 4.00e+02 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1088 2.81 - 3.33: 3098 3.33 - 3.86: 6567 3.86 - 4.38: 7546 4.38 - 4.90: 13461 Nonbonded interactions: 31760 Sorted by model distance: nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.288 3.040 nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.323 3.040 nonbonded pdb=" OG1 THR H 124 " pdb=" O ASP H 126 " model vdw 2.327 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.362 3.040 nonbonded pdb=" O SER H 147 " pdb=" OG SER H 147 " model vdw 2.374 3.040 ... (remaining 31755 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.920 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: 0.090 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.850 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.006 0.057 4129 Z= 0.279 Angle : 0.982 14.060 5626 Z= 0.500 Chirality : 0.063 0.483 635 Planarity : 0.007 0.069 705 Dihedral : 12.393 86.966 1425 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.37), residues: 483 helix: None (None), residues: 0 sheet: 0.15 (0.36), residues: 218 loop : -0.84 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 102 TYR 0.020 0.002 TYR A 160 PHE 0.028 0.003 PHE A 238 TRP 0.014 0.002 TRP H 66 HIS 0.005 0.002 HIS L 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.28 ( 4118) covalent geometry : angle 0.91645 / 0.49 ( 5597) SS BOND : bond 0.00134 / 0.07 ( 4) SS BOND : angle 2.20868 / 1.22 ( 8) hydrogen bonds : bond 0.09359 / 6.19 ( 139) hydrogen bonds : angle 6.77791 / 4.48 ( 357) link_BETA1-4 : bond 0.01131 / 0.60 ( 1) link_BETA1-4 : angle 2.94365 / 1.55 ( 3) link_NAG-ASN : bond 0.01313 / 0.66 ( 6) link_NAG-ASN : angle 6.06365 / 3.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.152 Fit side-chains REVERT: A 15 CYS cc_start: 0.7351 (m) cc_final: 0.7117 (m) REVERT: A 153 MET cc_start: 0.8371 (mmt) cc_final: 0.8037 (mmm) REVERT: H 99 TYR cc_start: 0.7958 (m-80) cc_final: 0.7599 (m-80) REVERT: L 63 GLN cc_start: 0.8931 (tt0) cc_final: 0.8671 (tt0) REVERT: L 75 LYS cc_start: 0.8501 (mttt) cc_final: 0.8168 (mtpt) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.4980 time to fit residues: 50.4916 Evaluate side-chains 83 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 0.0770 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 GLN L 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.122716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.080186 restraints weight = 6409.687| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 2.84 r_work: 0.2964 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4129 Z= 0.129 Angle : 0.647 10.524 5626 Z= 0.317 Chirality : 0.048 0.391 635 Planarity : 0.004 0.047 705 Dihedral : 5.095 25.003 537 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.38 % Allowed : 10.34 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.38), residues: 483 helix: None (None), residues: 0 sheet: 0.30 (0.35), residues: 218 loop : -0.38 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 86 TYR 0.009 0.001 TYR H 79 PHE 0.010 0.001 PHE A 133 TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 4118) covalent geometry : angle 0.60385 / 0.31 ( 5597) SS BOND : bond 0.00229 / 0.11 ( 4) SS BOND : angle 1.32502 / 0.75 ( 8) hydrogen bonds : bond 0.03420 / 2.09 ( 139) hydrogen bonds : angle 6.06089 / 4.02 ( 357) link_BETA1-4 : bond 0.00275 / 0.14 ( 1) link_BETA1-4 : angle 1.45823 / 0.75 ( 3) link_NAG-ASN : bond 0.00897 / 0.45 ( 6) link_NAG-ASN : angle 4.04588 / 2.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.153 Fit side-chains REVERT: A 129 LYS cc_start: 0.8248 (ttmm) cc_final: 0.8015 (ttmm) REVERT: A 214 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7339 (tpp-160) REVERT: H 42 LYS cc_start: 0.8923 (ttmm) cc_final: 0.8715 (tttp) REVERT: H 48 LEU cc_start: 0.8558 (tp) cc_final: 0.8213 (tt) REVERT: H 99 TYR cc_start: 0.8112 (m-80) cc_final: 0.7818 (m-80) REVERT: H 130 TYR cc_start: 0.8413 (m-80) cc_final: 0.8183 (m-80) REVERT: L 63 GLN cc_start: 0.8927 (tt0) cc_final: 0.8669 (tt0) REVERT: L 70 ARG cc_start: 0.8661 (ptt180) cc_final: 0.8435 (ppt170) REVERT: L 75 LYS cc_start: 0.8384 (mttt) cc_final: 0.8087 (mmmt) outliers start: 6 outliers final: 6 residues processed: 87 average time/residue: 0.4774 time to fit residues: 43.1034 Evaluate side-chains 85 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 2 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.122013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.079535 restraints weight = 6451.301| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.85 r_work: 0.2950 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4129 Z= 0.141 Angle : 0.619 10.038 5626 Z= 0.304 Chirality : 0.047 0.344 635 Planarity : 0.004 0.042 705 Dihedral : 4.704 20.314 537 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.30 % Allowed : 11.72 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.47 (0.37), residues: 215 loop : -0.10 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 86 TYR 0.012 0.001 TYR H 132 PHE 0.014 0.001 PHE A 175 TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 4118) covalent geometry : angle 0.58597 / 0.30 ( 5597) SS BOND : bond 0.00194 / 0.10 ( 4) SS BOND : angle 1.26790 / 0.71 ( 8) hydrogen bonds : bond 0.03149 / 1.93 ( 139) hydrogen bonds : angle 5.80703 / 3.86 ( 357) link_BETA1-4 : bond 0.00450 / 0.24 ( 1) link_BETA1-4 : angle 1.15572 / 0.60 ( 3) link_NAG-ASN : bond 0.00833 / 0.42 ( 6) link_NAG-ASN : angle 3.48701 / 2.25 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.113 Fit side-chains REVERT: A 215 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7634 (m-30) REVERT: H 48 LEU cc_start: 0.8620 (tp) cc_final: 0.8234 (tt) REVERT: H 50 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8078 (mp0) REVERT: H 65 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: H 100 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8082 (ttp) REVERT: H 130 TYR cc_start: 0.8448 (m-80) cc_final: 0.7922 (m-80) REVERT: L 63 GLN cc_start: 0.8895 (tt0) cc_final: 0.8555 (tt0) outliers start: 10 outliers final: 6 residues processed: 87 average time/residue: 0.4363 time to fit residues: 39.3741 Evaluate side-chains 88 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.120353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.077906 restraints weight = 6396.738| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.81 r_work: 0.2923 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4129 Z= 0.177 Angle : 0.638 10.908 5626 Z= 0.312 Chirality : 0.048 0.331 635 Planarity : 0.004 0.041 705 Dihedral : 4.671 18.103 537 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 5.06 % Allowed : 12.41 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.45 (0.37), residues: 209 loop : 0.10 (0.40), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 86 TYR 0.010 0.001 TYR A 269 PHE 0.019 0.002 PHE A 175 TRP 0.008 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 4118) covalent geometry : angle 0.60860 / 0.31 ( 5597) SS BOND : bond 0.00179 / 0.09 ( 4) SS BOND : angle 1.35224 / 0.73 ( 8) hydrogen bonds : bond 0.03239 / 2.01 ( 139) hydrogen bonds : angle 5.69285 / 3.78 ( 357) link_BETA1-4 : bond 0.00434 / 0.23 ( 1) link_BETA1-4 : angle 1.01478 / 0.52 ( 3) link_NAG-ASN : bond 0.00781 / 0.39 ( 6) link_NAG-ASN : angle 3.33371 / 2.16 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.195 Fit side-chains REVERT: A 218 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8038 (mp10) REVERT: H 48 LEU cc_start: 0.8606 (tp) cc_final: 0.8210 (tt) REVERT: H 65 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: H 83 PHE cc_start: 0.8484 (m-10) cc_final: 0.8141 (m-10) REVERT: H 100 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8169 (ttp) REVERT: H 130 TYR cc_start: 0.8552 (m-80) cc_final: 0.8057 (m-80) REVERT: L 63 GLN cc_start: 0.8943 (tt0) cc_final: 0.8617 (tt0) outliers start: 22 outliers final: 11 residues processed: 88 average time/residue: 0.4657 time to fit residues: 42.5396 Evaluate side-chains 90 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.120348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.077943 restraints weight = 6393.477| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.83 r_work: 0.2938 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4129 Z= 0.172 Angle : 0.643 11.460 5626 Z= 0.314 Chirality : 0.047 0.327 635 Planarity : 0.004 0.042 705 Dihedral : 4.615 17.301 537 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.91 % Allowed : 15.17 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.58 (0.38), residues: 198 loop : 0.10 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 86 TYR 0.012 0.001 TYR H 79 PHE 0.016 0.002 PHE A 175 TRP 0.005 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 ( 4118) covalent geometry : angle 0.61628 / 0.31 ( 5597) SS BOND : bond 0.00183 / 0.09 ( 4) SS BOND : angle 1.31019 / 0.73 ( 8) hydrogen bonds : bond 0.03211 / 1.99 ( 139) hydrogen bonds : angle 5.65670 / 3.77 ( 357) link_BETA1-4 : bond 0.00477 / 0.25 ( 1) link_BETA1-4 : angle 0.99265 / 0.51 ( 3) link_NAG-ASN : bond 0.00782 / 0.39 ( 6) link_NAG-ASN : angle 3.21797 / 2.09 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.157 Fit side-chains revert: symmetry clash REVERT: H 48 LEU cc_start: 0.8622 (tp) cc_final: 0.8244 (tt) REVERT: H 65 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7990 (pt0) REVERT: H 130 TYR cc_start: 0.8602 (m-80) cc_final: 0.8126 (m-80) REVERT: L 63 GLN cc_start: 0.8993 (tt0) cc_final: 0.8680 (tt0) outliers start: 17 outliers final: 14 residues processed: 82 average time/residue: 0.4823 time to fit residues: 41.1130 Evaluate side-chains 91 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.0000 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 39 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.121267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.078995 restraints weight = 6565.073| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.84 r_work: 0.2942 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4129 Z= 0.131 Angle : 0.618 11.914 5626 Z= 0.301 Chirality : 0.047 0.322 635 Planarity : 0.004 0.042 705 Dihedral : 4.417 16.819 537 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.14 % Allowed : 15.63 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.63 (0.38), residues: 203 loop : 0.15 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 86 TYR 0.012 0.001 TYR H 79 PHE 0.012 0.001 PHE A 175 TRP 0.006 0.001 TRP H 137 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 4118) covalent geometry : angle 0.59185 / 0.29 ( 5597) SS BOND : bond 0.00194 / 0.10 ( 4) SS BOND : angle 1.27678 / 0.70 ( 8) hydrogen bonds : bond 0.02981 / 1.83 ( 139) hydrogen bonds : angle 5.61514 / 3.75 ( 357) link_BETA1-4 : bond 0.00475 / 0.25 ( 1) link_BETA1-4 : angle 1.02137 / 0.53 ( 3) link_NAG-ASN : bond 0.00743 / 0.37 ( 6) link_NAG-ASN : angle 3.07358 / 2.01 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 131 CYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7570 (m) REVERT: A 211 ASN cc_start: 0.8627 (t0) cc_final: 0.8427 (t0) REVERT: A 215 ASP cc_start: 0.7914 (m-30) cc_final: 0.7596 (m-30) REVERT: A 218 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8029 (mp10) REVERT: H 48 LEU cc_start: 0.8522 (tp) cc_final: 0.8161 (tt) REVERT: H 65 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: H 130 TYR cc_start: 0.8624 (m-80) cc_final: 0.8175 (m-80) REVERT: L 55 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7089 (p0) REVERT: L 63 GLN cc_start: 0.8956 (tt0) cc_final: 0.8634 (tt0) outliers start: 18 outliers final: 12 residues processed: 82 average time/residue: 0.4536 time to fit residues: 38.7033 Evaluate side-chains 90 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 0.0050 chunk 4 optimal weight: 0.0060 chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.5410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.078912 restraints weight = 6507.617| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.82 r_work: 0.2939 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4129 Z= 0.140 Angle : 0.606 12.597 5626 Z= 0.298 Chirality : 0.046 0.323 635 Planarity : 0.004 0.041 705 Dihedral : 4.353 16.307 537 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.37 % Allowed : 15.86 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.58 (0.38), residues: 198 loop : 0.20 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 86 TYR 0.013 0.001 TYR H 132 PHE 0.017 0.001 PHE H 83 TRP 0.005 0.001 TRP H 137 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 4118) covalent geometry : angle 0.57954 / 0.29 ( 5597) SS BOND : bond 0.00157 / 0.08 ( 4) SS BOND : angle 1.27769 / 0.68 ( 8) hydrogen bonds : bond 0.03038 / 1.88 ( 139) hydrogen bonds : angle 5.61321 / 3.76 ( 357) link_BETA1-4 : bond 0.00459 / 0.24 ( 1) link_BETA1-4 : angle 0.97512 / 0.51 ( 3) link_NAG-ASN : bond 0.00755 / 0.38 ( 6) link_NAG-ASN : angle 3.06242 / 2.00 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.164 Fit side-chains revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7895 (m-30) cc_final: 0.7476 (m-30) REVERT: A 218 GLN cc_start: 0.8626 (OUTLIER) cc_final: 0.8019 (mp10) REVERT: H 48 LEU cc_start: 0.8541 (tp) cc_final: 0.8204 (tt) REVERT: H 65 GLU cc_start: 0.8310 (pt0) cc_final: 0.7954 (pt0) REVERT: H 102 LEU cc_start: 0.8152 (pt) cc_final: 0.7947 (pp) REVERT: H 130 TYR cc_start: 0.8635 (m-80) cc_final: 0.8223 (m-80) REVERT: L 55 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7251 (p0) REVERT: L 63 GLN cc_start: 0.8919 (tt0) cc_final: 0.8594 (tt0) outliers start: 19 outliers final: 12 residues processed: 83 average time/residue: 0.4479 time to fit residues: 38.6434 Evaluate side-chains 88 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.120314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.078049 restraints weight = 6479.061| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.80 r_work: 0.2930 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 4129 Z= 0.175 Angle : 0.640 13.432 5626 Z= 0.317 Chirality : 0.047 0.324 635 Planarity : 0.004 0.041 705 Dihedral : 4.572 18.829 537 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.14 % Allowed : 17.47 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.57 (0.38), residues: 199 loop : 0.12 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 86 TYR 0.016 0.001 TYR H 99 PHE 0.025 0.002 PHE H 83 TRP 0.006 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.17 ( 4118) covalent geometry : angle 0.61147 / 0.31 ( 5597) SS BOND : bond 0.00162 / 0.08 ( 4) SS BOND : angle 2.31697 / 1.28 ( 8) hydrogen bonds : bond 0.03055 / 1.92 ( 139) hydrogen bonds : angle 5.60063 / 3.74 ( 357) link_BETA1-4 : bond 0.00479 / 0.25 ( 1) link_BETA1-4 : angle 0.93448 / 0.49 ( 3) link_NAG-ASN : bond 0.00744 / 0.37 ( 6) link_NAG-ASN : angle 3.02100 / 1.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7935 (m-30) cc_final: 0.7515 (m-30) REVERT: A 218 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8039 (mp10) REVERT: H 48 LEU cc_start: 0.8585 (tp) cc_final: 0.8241 (tt) REVERT: H 65 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: H 102 LEU cc_start: 0.8182 (pt) cc_final: 0.7967 (pp) REVERT: L 55 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7269 (p0) REVERT: L 63 GLN cc_start: 0.8929 (tt0) cc_final: 0.8627 (tt0) outliers start: 18 outliers final: 13 residues processed: 81 average time/residue: 0.4359 time to fit residues: 36.6600 Evaluate side-chains 91 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 65 GLU Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.121363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.078550 restraints weight = 6519.367| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.86 r_work: 0.2939 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4129 Z= 0.139 Angle : 0.626 13.777 5626 Z= 0.313 Chirality : 0.047 0.313 635 Planarity : 0.004 0.041 705 Dihedral : 4.487 18.326 537 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.45 % Allowed : 18.16 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.53 (0.38), residues: 199 loop : 0.17 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 86 TYR 0.014 0.001 TYR H 132 PHE 0.028 0.001 PHE H 83 TRP 0.007 0.001 TRP H 66 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 4118) covalent geometry : angle 0.60034 / 0.31 ( 5597) SS BOND : bond 0.00137 / 0.07 ( 4) SS BOND : angle 1.83098 / 0.99 ( 8) hydrogen bonds : bond 0.02893 / 1.82 ( 139) hydrogen bonds : angle 5.59560 / 3.75 ( 357) link_BETA1-4 : bond 0.00491 / 0.26 ( 1) link_BETA1-4 : angle 0.99965 / 0.52 ( 3) link_NAG-ASN : bond 0.00709 / 0.35 ( 6) link_NAG-ASN : angle 2.96600 / 1.95 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7876 (m-30) cc_final: 0.7469 (m-30) REVERT: A 218 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: H 48 LEU cc_start: 0.8565 (tp) cc_final: 0.8228 (tt) REVERT: H 102 LEU cc_start: 0.8102 (pt) cc_final: 0.7891 (pp) REVERT: H 130 TYR cc_start: 0.8622 (m-80) cc_final: 0.8215 (m-80) REVERT: L 55 ASN cc_start: 0.8158 (m110) cc_final: 0.7269 (p0) REVERT: L 63 GLN cc_start: 0.8898 (tt0) cc_final: 0.8591 (tt0) outliers start: 15 outliers final: 10 residues processed: 84 average time/residue: 0.3899 time to fit residues: 34.0715 Evaluate side-chains 83 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.120570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.078085 restraints weight = 6446.508| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.80 r_work: 0.2923 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4129 Z= 0.173 Angle : 0.668 14.108 5626 Z= 0.330 Chirality : 0.048 0.318 635 Planarity : 0.004 0.041 705 Dihedral : 4.598 17.678 537 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.22 % Allowed : 19.08 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.53 (0.38), residues: 199 loop : 0.14 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 86 TYR 0.014 0.001 TYR H 132 PHE 0.037 0.002 PHE H 83 TRP 0.008 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 ( 4118) covalent geometry : angle 0.64410 / 0.32 ( 5597) SS BOND : bond 0.00106 / 0.05 ( 4) SS BOND : angle 1.74463 / 0.95 ( 8) hydrogen bonds : bond 0.03072 / 1.94 ( 139) hydrogen bonds : angle 5.64808 / 3.79 ( 357) link_BETA1-4 : bond 0.00440 / 0.23 ( 1) link_BETA1-4 : angle 0.91590 / 0.48 ( 3) link_NAG-ASN : bond 0.00739 / 0.37 ( 6) link_NAG-ASN : angle 3.00631 / 1.97 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 966 Ramachandran restraints generated. 483 Oldfield, 0 Emsley, 483 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.7923 (m-30) cc_final: 0.7476 (m-30) REVERT: A 218 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: H 48 LEU cc_start: 0.8548 (tp) cc_final: 0.8215 (tt) REVERT: H 130 TYR cc_start: 0.8630 (m-80) cc_final: 0.8293 (m-80) REVERT: L 55 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7299 (p0) REVERT: L 63 GLN cc_start: 0.8964 (tt0) cc_final: 0.8652 (tt0) REVERT: L 70 ARG cc_start: 0.8683 (ptt180) cc_final: 0.8188 (ppt-90) outliers start: 14 outliers final: 9 residues processed: 79 average time/residue: 0.4485 time to fit residues: 36.7291 Evaluate side-chains 84 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 103 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 122 THR Chi-restraints excluded: chain L residue 129 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.121053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.078508 restraints weight = 6424.284| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.83 r_work: 0.2931 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4129 Z= 0.153 Angle : 0.658 14.110 5626 Z= 0.327 Chirality : 0.047 0.317 635 Planarity : 0.004 0.040 705 Dihedral : 4.556 17.034 537 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.53 % Allowed : 19.54 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.48 (0.38), residues: 199 loop : 0.16 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 86 TYR 0.014 0.001 TYR H 132 PHE 0.013 0.001 PHE A 175 TRP 0.008 0.001 TRP H 66 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 4118) covalent geometry : angle 0.63496 / 0.32 ( 5597) SS BOND : bond 0.00146 / 0.07 ( 4) SS BOND : angle 1.60245 / 0.87 ( 8) hydrogen bonds : bond 0.02937 / 1.84 ( 139) hydrogen bonds : angle 5.63181 / 3.78 ( 357) link_BETA1-4 : bond 0.00497 / 0.26 ( 1) link_BETA1-4 : angle 0.96818 / 0.50 ( 3) link_NAG-ASN : bond 0.00716 / 0.36 ( 6) link_NAG-ASN : angle 2.96194 / 1.94 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2071.89 seconds wall clock time: 36 minutes 0.25 seconds (2160.25 seconds total)