Starting phenix.real_space_refine on Sat Apr 4 21:36:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dls_27514/04_2026/8dls_27514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dls_27514/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dls_27514/04_2026/8dls_27514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dls_27514/04_2026/8dls_27514.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dls_27514/04_2026/8dls_27514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dls_27514/04_2026/8dls_27514.map" } 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-2.1rc1-6017/lib/python3.9/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 dihedrals: 6 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.10, per 1000 atoms: 0.27 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: 0.30 Conformation dependent library (CDL) restraints added in 132.3 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: 0.17 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: 0.64 Time building geometry restraints manager: 0.42 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: 2319 17.40 - 34.79: 149 34.79 - 52.18: 26 52.18 - 69.57: 5 69.57 - 86.97: 5 Dihedral angle restraints: 2504 sinusoidal: 1066 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 2501 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: 5.690 Set stop_for_unknowns flag: 0.010 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.950 Find NCS groups from input model: 0.030 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:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 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 : 12.285 86.966 1572 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 covalent geometry : bond 0.00614 ( 4118) covalent geometry : angle 0.91645 ( 5597) SS BOND : bond 0.00134 ( 4) SS BOND : angle 2.20868 ( 8) hydrogen bonds : bond 0.09359 ( 139) hydrogen bonds : angle 6.77791 ( 357) link_BETA1-4 : bond 0.01131 ( 1) link_BETA1-4 : angle 2.94365 ( 3) link_NAG-ASN : bond 0.01313 ( 6) link_NAG-ASN : angle 6.06365 ( 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 : 0.096 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: 0.4819 time to fit residues: 48.8639 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 : 0.158 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.122732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.080283 restraints weight = 6414.020| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.84 r_work: 0.2961 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4129 Z= 0.130 Angle : 0.646 10.474 5626 Z= 0.317 Chirality : 0.049 0.388 635 Planarity : 0.004 0.048 705 Dihedral : 6.241 50.760 684 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.38 % Allowed : 10.11 % Favored : 88.51 % 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 (0.39), residues: 483 helix: None (None), residues: 0 sheet: 0.30 (0.35), residues: 218 loop : -0.37 (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 A 269 PHE 0.010 0.001 PHE A 133 TRP 0.012 0.001 TRP H 66 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 4118) covalent geometry : angle 0.60127 ( 5597) SS BOND : bond 0.00235 ( 4) SS BOND : angle 1.33004 ( 8) hydrogen bonds : bond 0.03445 ( 139) hydrogen bonds : angle 6.05486 ( 357) link_BETA1-4 : bond 0.00260 ( 1) link_BETA1-4 : angle 1.50047 ( 3) link_NAG-ASN : bond 0.00988 ( 6) link_NAG-ASN : angle 4.11368 ( 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 : 0.158 Fit side-chains REVERT: A 129 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7937 (ttmm) REVERT: A 214 ARG cc_start: 0.7729 (tpp-160) cc_final: 0.7351 (tpp-160) REVERT: H 42 LYS cc_start: 0.8878 (ttmm) cc_final: 0.8673 (tttp) REVERT: H 99 TYR cc_start: 0.8069 (m-80) cc_final: 0.7772 (m-80) REVERT: H 130 TYR cc_start: 0.8433 (m-80) cc_final: 0.8133 (m-80) REVERT: L 63 GLN cc_start: 0.8890 (tt0) cc_final: 0.8623 (tt0) REVERT: L 75 LYS cc_start: 0.8319 (mttt) cc_final: 0.8022 (mmmt) outliers start: 6 outliers final: 6 residues processed: 87 average time/residue: 0.4875 time to fit residues: 43.9305 Evaluate side-chains 86 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 80 time to evaluate : 0.153 ------------------------------------------------------------------------------- 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: 0.0070 chunk 31 optimal weight: 4.9990 chunk 26 optimal weight: 0.0970 chunk 29 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.122713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.080383 restraints weight = 6449.714| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.86 r_work: 0.2970 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1513 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= 0.121 Angle : 0.612 10.076 5626 Z= 0.300 Chirality : 0.047 0.350 635 Planarity : 0.004 0.042 705 Dihedral : 5.877 50.535 684 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: 0.14 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.47 (0.36), residues: 215 loop : -0.14 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 86 TYR 0.011 0.001 TYR H 132 PHE 0.010 0.001 PHE A 175 TRP 0.010 0.001 TRP H 66 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 4118) covalent geometry : angle 0.57529 ( 5597) SS BOND : bond 0.00248 ( 4) SS BOND : angle 1.23963 ( 8) hydrogen bonds : bond 0.03111 ( 139) hydrogen bonds : angle 5.85128 ( 357) link_BETA1-4 : bond 0.00383 ( 1) link_BETA1-4 : angle 1.49126 ( 3) link_NAG-ASN : bond 0.00882 ( 6) link_NAG-ASN : angle 3.62506 ( 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 94 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.150 Fit side-chains REVERT: A 129 LYS cc_start: 0.8246 (ttmm) cc_final: 0.8044 (ttmm) REVERT: A 214 ARG cc_start: 0.7773 (tpp-160) cc_final: 0.7230 (tmt170) REVERT: A 215 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: H 48 LEU cc_start: 0.8533 (tp) cc_final: 0.8189 (tt) REVERT: H 99 TYR cc_start: 0.8093 (m-80) cc_final: 0.7864 (m-80) REVERT: H 100 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.8053 (ttp) REVERT: H 130 TYR cc_start: 0.8427 (m-80) cc_final: 0.8008 (m-80) REVERT: L 63 GLN cc_start: 0.8935 (tt0) cc_final: 0.8576 (tt0) outliers start: 10 outliers final: 7 residues processed: 85 average time/residue: 0.4767 time to fit residues: 42.0489 Evaluate side-chains 89 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain H residue 36 SER 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 103 VAL 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: 0.0470 chunk 12 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.121274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078918 restraints weight = 6373.732| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.82 r_work: 0.2943 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4129 Z= 0.151 Angle : 0.617 10.557 5626 Z= 0.303 Chirality : 0.047 0.333 635 Planarity : 0.004 0.041 705 Dihedral : 5.692 49.041 684 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 13.10 % Favored : 83.45 % 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: 0.47 (0.37), residues: 215 loop : 0.08 (0.41), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 86 TYR 0.014 0.001 TYR H 79 PHE 0.016 0.002 PHE L 96 TRP 0.009 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4118) covalent geometry : angle 0.58492 ( 5597) SS BOND : bond 0.00158 ( 4) SS BOND : angle 1.17106 ( 8) hydrogen bonds : bond 0.03126 ( 139) hydrogen bonds : angle 5.63679 ( 357) link_BETA1-4 : bond 0.00461 ( 1) link_BETA1-4 : angle 1.35338 ( 3) link_NAG-ASN : bond 0.00792 ( 6) link_NAG-ASN : angle 3.39214 ( 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 99 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.132 Fit side-chains REVERT: A 211 ASN cc_start: 0.8751 (t0) cc_final: 0.8520 (t0) REVERT: A 214 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7270 (tmt170) REVERT: A 215 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7619 (m-30) REVERT: H 42 LYS cc_start: 0.8927 (ttmm) cc_final: 0.8726 (tttp) REVERT: H 48 LEU cc_start: 0.8545 (tp) cc_final: 0.8154 (tt) REVERT: H 65 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: H 100 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.8052 (ttp) REVERT: H 130 TYR cc_start: 0.8516 (m-80) cc_final: 0.8025 (m-80) REVERT: L 63 GLN cc_start: 0.8962 (tt0) cc_final: 0.8618 (tt0) outliers start: 15 outliers final: 7 residues processed: 88 average time/residue: 0.4950 time to fit residues: 45.0990 Evaluate side-chains 88 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.169 ------------------------------------------------------------------------------- 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 23 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.0970 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.0470 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 10.0000 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.4980 overall best weight: 0.4676 ------------------------------------------------------------------------------- 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 = 0.3741 r_free = 0.3741 target = 0.121655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.079618 restraints weight = 6377.634| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.80 r_work: 0.2953 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4129 Z= 0.132 Angle : 0.617 11.226 5626 Z= 0.301 Chirality : 0.046 0.326 635 Planarity : 0.004 0.042 705 Dihedral : 5.652 49.589 684 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.91 % Allowed : 14.25 % Favored : 81.84 % 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: 0.59 (0.37), residues: 204 loop : 0.05 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 86 TYR 0.008 0.001 TYR A 269 PHE 0.013 0.001 PHE L 96 TRP 0.008 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 4118) covalent geometry : angle 0.58858 ( 5597) SS BOND : bond 0.00170 ( 4) SS BOND : angle 1.58282 ( 8) hydrogen bonds : bond 0.02953 ( 139) hydrogen bonds : angle 5.60146 ( 357) link_BETA1-4 : bond 0.00457 ( 1) link_BETA1-4 : angle 1.33518 ( 3) link_NAG-ASN : bond 0.00773 ( 6) link_NAG-ASN : angle 3.14515 ( 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 94 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.140 Fit side-chains REVERT: A 214 ARG cc_start: 0.7867 (tpp-160) cc_final: 0.7237 (tmt170) REVERT: A 215 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: A 218 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8001 (mp10) REVERT: H 48 LEU cc_start: 0.8563 (tp) cc_final: 0.8184 (tt) REVERT: H 65 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: H 83 PHE cc_start: 0.8288 (m-10) cc_final: 0.7893 (m-10) REVERT: H 100 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8135 (ttp) REVERT: H 130 TYR cc_start: 0.8520 (m-80) cc_final: 0.8049 (m-80) REVERT: L 63 GLN cc_start: 0.8961 (tt0) cc_final: 0.8623 (tt0) outliers start: 17 outliers final: 8 residues processed: 83 average time/residue: 0.5128 time to fit residues: 44.1493 Evaluate side-chains 85 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP 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 118 SER Chi-restraints excluded: chain H residue 134 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.120275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.077803 restraints weight = 6627.621| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.84 r_work: 0.2920 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4129 Z= 0.183 Angle : 0.643 12.068 5626 Z= 0.314 Chirality : 0.047 0.328 635 Planarity : 0.004 0.041 705 Dihedral : 5.677 47.556 684 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.37 % Allowed : 15.17 % Favored : 80.46 % 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: 0.44 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.63 (0.38), residues: 198 loop : 0.14 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 86 TYR 0.010 0.001 TYR A 269 PHE 0.018 0.002 PHE A 175 TRP 0.006 0.001 TRP H 66 HIS 0.002 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 4118) covalent geometry : angle 0.61598 ( 5597) SS BOND : bond 0.00147 ( 4) SS BOND : angle 1.22882 ( 8) hydrogen bonds : bond 0.03159 ( 139) hydrogen bonds : angle 5.59404 ( 357) link_BETA1-4 : bond 0.00431 ( 1) link_BETA1-4 : angle 1.20365 ( 3) link_NAG-ASN : bond 0.00775 ( 6) link_NAG-ASN : angle 3.19420 ( 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 94 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.167 Fit side-chains revert: symmetry clash REVERT: A 211 ASN cc_start: 0.8777 (t0) cc_final: 0.8571 (t0) REVERT: A 214 ARG cc_start: 0.7938 (tpp-160) cc_final: 0.7220 (tpt90) REVERT: A 218 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: H 48 LEU cc_start: 0.8622 (tp) cc_final: 0.8241 (tt) REVERT: H 100 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.8102 (ttp) REVERT: H 130 TYR cc_start: 0.8642 (m-80) cc_final: 0.8222 (m-80) REVERT: L 63 GLN cc_start: 0.8996 (tt0) cc_final: 0.8685 (tt0) outliers start: 19 outliers final: 13 residues processed: 79 average time/residue: 0.4918 time to fit residues: 40.2758 Evaluate side-chains 90 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 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 100 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 32 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 4 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.120508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.078218 restraints weight = 6504.828| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.80 r_work: 0.2927 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4129 Z= 0.167 Angle : 0.630 12.302 5626 Z= 0.306 Chirality : 0.047 0.324 635 Planarity : 0.004 0.041 705 Dihedral : 5.645 47.346 684 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 4.83 % Allowed : 14.94 % 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: 0.47 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.63 (0.38), residues: 199 loop : 0.17 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 86 TYR 0.016 0.001 TYR H 99 PHE 0.016 0.001 PHE A 175 TRP 0.005 0.001 TRP A 104 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 4118) covalent geometry : angle 0.60328 ( 5597) SS BOND : bond 0.00138 ( 4) SS BOND : angle 1.05926 ( 8) hydrogen bonds : bond 0.03048 ( 139) hydrogen bonds : angle 5.58180 ( 357) link_BETA1-4 : bond 0.00398 ( 1) link_BETA1-4 : angle 1.18951 ( 3) link_NAG-ASN : bond 0.00763 ( 6) link_NAG-ASN : angle 3.16050 ( 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 96 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.168 Fit side-chains REVERT: A 214 ARG cc_start: 0.7915 (tpp-160) cc_final: 0.7224 (tpt90) REVERT: A 218 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8058 (mp10) REVERT: H 48 LEU cc_start: 0.8636 (tp) cc_final: 0.8266 (tt) REVERT: H 100 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8098 (ttp) REVERT: H 130 TYR cc_start: 0.8625 (m-80) cc_final: 0.8228 (m-80) REVERT: L 55 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7209 (p0) REVERT: L 63 GLN cc_start: 0.8993 (tt0) cc_final: 0.8684 (tt0) outliers start: 21 outliers final: 13 residues processed: 82 average time/residue: 0.5059 time to fit residues: 42.9938 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 : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL 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 36 SER Chi-restraints excluded: chain H residue 100 MET 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 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: 0.5980 chunk 14 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.120127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.077699 restraints weight = 6437.824| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.79 r_work: 0.2934 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2212 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= 0.182 Angle : 0.659 13.323 5626 Z= 0.322 Chirality : 0.048 0.325 635 Planarity : 0.004 0.041 705 Dihedral : 5.704 46.418 684 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.14 % Allowed : 16.09 % 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: 0.47 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.61 (0.38), residues: 199 loop : 0.19 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 86 TYR 0.012 0.001 TYR H 79 PHE 0.018 0.001 PHE A 175 TRP 0.005 0.001 TRP H 66 HIS 0.002 0.001 HIS H 54 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 4118) covalent geometry : angle 0.63363 ( 5597) SS BOND : bond 0.00131 ( 4) SS BOND : angle 1.05493 ( 8) hydrogen bonds : bond 0.03145 ( 139) hydrogen bonds : angle 5.58550 ( 357) link_BETA1-4 : bond 0.00425 ( 1) link_BETA1-4 : angle 1.13929 ( 3) link_NAG-ASN : bond 0.00766 ( 6) link_NAG-ASN : angle 3.16046 ( 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 : 0.177 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7961 (tpp-160) cc_final: 0.7229 (tpt90) REVERT: A 215 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: A 218 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8033 (mp10) REVERT: H 48 LEU cc_start: 0.8567 (tp) cc_final: 0.8213 (tt) REVERT: H 50 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8560 (mt-10) REVERT: H 83 PHE cc_start: 0.7753 (m-10) cc_final: 0.7484 (m-10) REVERT: L 55 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7161 (p0) REVERT: L 63 GLN cc_start: 0.8973 (tt0) cc_final: 0.8657 (tt0) outliers start: 18 outliers final: 14 residues processed: 81 average time/residue: 0.5185 time to fit residues: 43.5351 Evaluate side-chains 91 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 215 ASP 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 36 SER 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 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: 3.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 26 optimal weight: 0.0020 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.120864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.078739 restraints weight = 6467.550| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.80 r_work: 0.2941 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4129 Z= 0.149 Angle : 0.642 13.566 5626 Z= 0.317 Chirality : 0.047 0.313 635 Planarity : 0.004 0.041 705 Dihedral : 5.632 47.436 684 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.14 % Allowed : 16.55 % Favored : 79.31 % 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: 0.41 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.54 (0.38), residues: 199 loop : 0.18 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 86 TYR 0.014 0.001 TYR H 99 PHE 0.013 0.001 PHE A 175 TRP 0.005 0.001 TRP H 137 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4118) covalent geometry : angle 0.61794 ( 5597) SS BOND : bond 0.00125 ( 4) SS BOND : angle 1.02301 ( 8) hydrogen bonds : bond 0.02953 ( 139) hydrogen bonds : angle 5.57415 ( 357) link_BETA1-4 : bond 0.00447 ( 1) link_BETA1-4 : angle 1.19256 ( 3) link_NAG-ASN : bond 0.00743 ( 6) link_NAG-ASN : angle 3.05511 ( 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 96 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.115 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7269 (tpt90) REVERT: A 218 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: H 48 LEU cc_start: 0.8561 (tp) cc_final: 0.8195 (tt) REVERT: H 50 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8539 (mt-10) REVERT: H 130 TYR cc_start: 0.8612 (m-80) cc_final: 0.8201 (m-80) REVERT: L 55 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7181 (p0) REVERT: L 63 GLN cc_start: 0.8955 (tt0) cc_final: 0.8634 (tt0) REVERT: L 70 ARG cc_start: 0.8672 (ptt180) cc_final: 0.8169 (ppt-90) outliers start: 18 outliers final: 12 residues processed: 84 average time/residue: 0.4371 time to fit residues: 38.0972 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 : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 131 CYS 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 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 50 VAL Chi-restraints excluded: chain L residue 55 ASN Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 108 VAL 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: 0.9980 chunk 24 optimal weight: 0.4980 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.120569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.078323 restraints weight = 6460.746| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.79 r_work: 0.2932 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4129 Z= 0.161 Angle : 0.662 14.042 5626 Z= 0.326 Chirality : 0.048 0.314 635 Planarity : 0.004 0.044 705 Dihedral : 5.617 47.054 684 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.68 % Allowed : 17.47 % Favored : 78.85 % 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: 0.34 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.52 (0.38), residues: 199 loop : 0.11 (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 0.015 0.001 PHE A 175 TRP 0.006 0.001 TRP H 66 HIS 0.002 0.001 HIS L 51 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 4118) covalent geometry : angle 0.63870 ( 5597) SS BOND : bond 0.00139 ( 4) SS BOND : angle 1.04571 ( 8) hydrogen bonds : bond 0.03033 ( 139) hydrogen bonds : angle 5.59741 ( 357) link_BETA1-4 : bond 0.00412 ( 1) link_BETA1-4 : angle 1.16916 ( 3) link_NAG-ASN : bond 0.00751 ( 6) link_NAG-ASN : angle 3.03812 ( 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 91 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.148 Fit side-chains revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7934 (tpp-160) cc_final: 0.7230 (tpt90) REVERT: A 218 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: H 31 LYS cc_start: 0.8257 (ptpp) cc_final: 0.7850 (pttt) REVERT: H 48 LEU cc_start: 0.8580 (tp) cc_final: 0.8216 (tt) REVERT: H 50 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8586 (mt-10) REVERT: H 130 TYR cc_start: 0.8596 (m-80) cc_final: 0.8191 (m-80) REVERT: L 55 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7249 (p0) REVERT: L 63 GLN cc_start: 0.8985 (tt0) cc_final: 0.8631 (tt0) REVERT: L 70 ARG cc_start: 0.8681 (ptt180) cc_final: 0.8380 (ppt-90) outliers start: 16 outliers final: 12 residues processed: 80 average time/residue: 0.4334 time to fit residues: 36.0014 Evaluate side-chains 89 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL 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 26 SER 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 134 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 108 VAL 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: 0.7980 chunk 2 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.0570 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.121046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.078852 restraints weight = 6463.776| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.81 r_work: 0.2945 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4129 Z= 0.143 Angle : 0.662 14.106 5626 Z= 0.324 Chirality : 0.047 0.313 635 Planarity : 0.004 0.041 705 Dihedral : 5.578 47.842 684 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.45 % Allowed : 17.70 % Favored : 78.85 % 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: 0.33 (0.40), residues: 483 helix: None (None), residues: 0 sheet: 0.48 (0.38), residues: 199 loop : 0.13 (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 0.012 0.001 PHE A 175 TRP 0.007 0.001 TRP H 66 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4118) covalent geometry : angle 0.63955 ( 5597) SS BOND : bond 0.00152 ( 4) SS BOND : angle 1.02647 ( 8) hydrogen bonds : bond 0.02946 ( 139) hydrogen bonds : angle 5.56316 ( 357) link_BETA1-4 : bond 0.00389 ( 1) link_BETA1-4 : angle 1.20422 ( 3) link_NAG-ASN : bond 0.00743 ( 6) link_NAG-ASN : angle 2.99459 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2194.64 seconds wall clock time: 38 minutes 3.72 seconds (2283.72 seconds total)