Starting phenix.real_space_refine on Sat May 10 07:21:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eai_47832/05_2025/9eai_47832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eai_47832/05_2025/9eai_47832.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eai_47832/05_2025/9eai_47832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eai_47832/05_2025/9eai_47832.map" model { file = "/net/cci-nas-00/data/ceres_data/9eai_47832/05_2025/9eai_47832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eai_47832/05_2025/9eai_47832.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 Cl 1 4.86 5 C 3653 2.51 5 N 883 2.21 5 O 991 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5554 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2976 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 13, 'TRANS': 359} Chain breaks: 2 Chain: "B" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 681 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain breaks: 5 Chain: "C" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 944 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 117} Chain: "D" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 839 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "A" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 114 Unusual residues: {'CLR': 1, 'LSN': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.45, per 1000 atoms: 0.80 Number of scatterers: 5554 At special positions: 0 Unit cell: (83.83, 91.3, 136.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 26 16.00 O 991 8.00 N 883 7.00 C 3653 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 94 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " 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 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 853.8 milliseconds 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1294 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 9 sheets defined 47.6% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 29 through 56 removed outlier: 3.504A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 48 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 90 Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 97 through 132 removed outlier: 3.543A pdb=" N SER A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 160 removed outlier: 3.739A pdb=" N GLY A 157 " --> pdb=" O TRP A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 190 through 201 Processing helix chain 'A' and resid 204 through 244 Processing helix chain 'A' and resid 247 through 267 removed outlier: 3.600A pdb=" N VAL A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 306 Processing helix chain 'A' and resid 309 through 326 removed outlier: 4.218A pdb=" N LYS A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N THR A 321 " --> pdb=" O GLU A 317 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N THR A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ARG A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 340 Processing helix chain 'A' and resid 1238 through 1253 Processing helix chain 'A' and resid 1253 through 1268 Processing helix chain 'A' and resid 1273 through 1291 Proline residue: A1285 - end of helix Processing helix chain 'A' and resid 1293 through 1305 Proline residue: A1299 - end of helix removed outlier: 3.848A pdb=" N TYR A1302 " --> pdb=" O ASN A1298 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A1303 " --> pdb=" O PRO A1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 removed outlier: 3.785A pdb=" N THR C 94 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.874A pdb=" N TRP C 111 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 removed outlier: 4.154A pdb=" N VAL D 98 " --> pdb=" O TYR D 95 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.681A pdb=" N VAL B 91 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N MET B 33 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY B 49 " --> pdb=" O MET B 33 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP B 35 " --> pdb=" O VAL B 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 171 removed outlier: 3.690A pdb=" N TYR B 92 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 18 through 20 removed outlier: 3.609A pdb=" N THR B 67 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 7 Processing sheet with id=AA5, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=AA6, first strand: chain 'C' and resid 61 through 63 removed outlier: 6.760A pdb=" N TRP C 39 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N TYR C 53 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 14 removed outlier: 3.540A pdb=" N TYR D 87 " --> pdb=" O THR D 104 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 47 through 49 removed outlier: 6.515A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 2.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1041 1.33 - 1.45: 1495 1.45 - 1.57: 3122 1.57 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 5697 Sorted by residual: bond pdb=" C17 LSN A1401 " pdb="CL LSN A1401 " ideal model delta sigma weight residual 1.717 1.783 -0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C15 LSN A1401 " pdb=" N5 LSN A1401 " ideal model delta sigma weight residual 1.379 1.317 0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" N1 LSN A1401 " pdb=" N2 LSN A1401 " ideal model delta sigma weight residual 1.290 1.352 -0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" C1 LSN A1401 " pdb=" C2 LSN A1401 " ideal model delta sigma weight residual 1.466 1.525 -0.059 2.00e-02 2.50e+03 8.74e+00 bond pdb=" C7 LSN A1401 " pdb=" C8 LSN A1401 " ideal model delta sigma weight residual 1.479 1.531 -0.052 2.00e-02 2.50e+03 6.64e+00 ... (remaining 5692 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 7563 1.31 - 2.62: 151 2.62 - 3.93: 25 3.93 - 5.25: 16 5.25 - 6.56: 3 Bond angle restraints: 7758 Sorted by residual: angle pdb=" N VAL C 67 " pdb=" CA VAL C 67 " pdb=" C VAL C 67 " ideal model delta sigma weight residual 113.20 109.56 3.64 9.60e-01 1.09e+00 1.44e+01 angle pdb=" N2 LSN A1401 " pdb=" N3 LSN A1401 " pdb=" N4 LSN A1401 " ideal model delta sigma weight residual 114.47 107.91 6.56 3.00e+00 1.11e-01 4.78e+00 angle pdb=" CA LEU A 161 " pdb=" C LEU A 161 " pdb=" N PRO A 162 " ideal model delta sigma weight residual 118.44 121.90 -3.46 1.59e+00 3.96e-01 4.73e+00 angle pdb=" N LEU A 161 " pdb=" CA LEU A 161 " pdb=" C LEU A 161 " ideal model delta sigma weight residual 109.81 114.50 -4.69 2.21e+00 2.05e-01 4.51e+00 angle pdb=" C1 LSN A1401 " pdb=" N4 LSN A1401 " pdb=" N3 LSN A1401 " ideal model delta sigma weight residual 101.68 108.00 -6.32 3.00e+00 1.11e-01 4.44e+00 ... (remaining 7753 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.31: 3229 15.31 - 30.62: 171 30.62 - 45.92: 46 45.92 - 61.23: 15 61.23 - 76.54: 2 Dihedral angle restraints: 3463 sinusoidal: 1450 harmonic: 2013 Sorted by residual: dihedral pdb=" CA ASP D 71 " pdb=" CB ASP D 71 " pdb=" CG ASP D 71 " pdb=" OD1 ASP D 71 " ideal model delta sinusoidal sigma weight residual -30.00 -86.19 56.19 1 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" N LEU A 191 " pdb=" CA LEU A 191 " pdb=" CB LEU A 191 " pdb=" CG LEU A 191 " ideal model delta sinusoidal sigma weight residual -180.00 -121.97 -58.03 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" CA LYS A 329 " pdb=" CB LYS A 329 " pdb=" CG LYS A 329 " pdb=" CD LYS A 329 " ideal model delta sinusoidal sigma weight residual 180.00 122.04 57.96 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 3460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 561 0.029 - 0.059: 214 0.059 - 0.088: 73 0.088 - 0.118: 35 0.118 - 0.147: 3 Chirality restraints: 886 Sorted by residual: chirality pdb=" CA ILE D 49 " pdb=" N ILE D 49 " pdb=" C ILE D 49 " pdb=" CB ILE D 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE D 76 " pdb=" N ILE D 76 " pdb=" C ILE D 76 " pdb=" CB ILE D 76 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE A1238 " pdb=" N ILE A1238 " pdb=" C ILE A1238 " pdb=" CB ILE A1238 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 883 not shown) Planarity restraints: 936 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 108 " -0.029 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO C 109 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO A 95 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 44 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO D 45 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 45 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 45 " -0.018 5.00e-02 4.00e+02 ... (remaining 933 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 944 2.77 - 3.30: 5341 3.30 - 3.83: 9272 3.83 - 4.37: 11071 4.37 - 4.90: 19655 Nonbonded interactions: 46283 Sorted by model distance: nonbonded pdb=" OE1 GLN A 296 " pdb=" OG1 THR A 322 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 55 " pdb=" OH TYR C 104 " model vdw 2.266 3.040 nonbonded pdb=" O TYR D 50 " pdb=" OH TYR D 92 " model vdw 2.274 3.040 nonbonded pdb=" O GLY A 196 " pdb=" ND2 ASN A 200 " model vdw 2.286 3.120 nonbonded pdb=" N ASN B 98 " pdb=" OD1 ASN B 98 " model vdw 2.290 3.120 ... (remaining 46278 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: 3.430 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.410 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.003 0.066 5701 Z= 0.164 Angle : 0.512 6.558 7766 Z= 0.254 Chirality : 0.038 0.147 886 Planarity : 0.003 0.043 936 Dihedral : 10.650 76.538 2157 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.37 % Allowed : 6.51 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.34), residues: 665 helix: 1.55 (0.31), residues: 301 sheet: -1.19 (0.45), residues: 145 loop : -0.96 (0.44), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 232 HIS 0.002 0.001 HIS A 166 PHE 0.014 0.001 PHE A 286 TYR 0.014 0.001 TYR D 92 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.16733 ( 302) hydrogen bonds : angle 6.75640 ( 888) SS BOND : bond 0.00159 ( 4) SS BOND : angle 1.19482 ( 8) covalent geometry : bond 0.00348 ( 5697) covalent geometry : angle 0.51047 ( 7758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.592 Fit side-chains REVERT: A 101 CYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8204 (t) REVERT: A 216 THR cc_start: 0.8026 (m) cc_final: 0.7790 (m) REVERT: A 237 ASP cc_start: 0.7034 (m-30) cc_final: 0.6777 (m-30) REVERT: A 283 MET cc_start: 0.7985 (tpp) cc_final: 0.7640 (tpt) REVERT: D 5 MET cc_start: 0.8516 (mmm) cc_final: 0.7920 (mmt) REVERT: D 110 ARG cc_start: 0.5481 (mtt180) cc_final: 0.3055 (ptt-90) outliers start: 8 outliers final: 6 residues processed: 82 average time/residue: 0.1494 time to fit residues: 16.8982 Evaluate side-chains 73 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 CYS Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 98 ASN Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 60 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: A 132 HIS A1235 ASN D 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.180444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.141947 restraints weight = 5915.482| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.11 r_work: 0.3429 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5701 Z= 0.156 Angle : 0.519 5.086 7766 Z= 0.269 Chirality : 0.040 0.144 886 Planarity : 0.004 0.044 936 Dihedral : 6.586 60.177 968 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.05 % Allowed : 9.42 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.34), residues: 665 helix: 1.67 (0.30), residues: 305 sheet: -1.29 (0.43), residues: 153 loop : -0.93 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 232 HIS 0.003 0.001 HIS A 132 PHE 0.015 0.001 PHE A 286 TYR 0.016 0.002 TYR D 50 ARG 0.002 0.000 ARG A 259 Details of bonding type rmsd hydrogen bonds : bond 0.04639 ( 302) hydrogen bonds : angle 4.64223 ( 888) SS BOND : bond 0.00171 ( 4) SS BOND : angle 1.27378 ( 8) covalent geometry : bond 0.00356 ( 5697) covalent geometry : angle 0.51775 ( 7758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.576 Fit side-chains REVERT: A 168 ASN cc_start: 0.8245 (m-40) cc_final: 0.7972 (m-40) REVERT: A 200 ASN cc_start: 0.8062 (m-40) cc_final: 0.7755 (m-40) REVERT: A 216 THR cc_start: 0.7966 (m) cc_final: 0.7732 (m) REVERT: A 237 ASP cc_start: 0.7017 (m-30) cc_final: 0.6701 (m-30) REVERT: A 283 MET cc_start: 0.7961 (tpp) cc_final: 0.7604 (tpt) REVERT: D 49 ILE cc_start: 0.9034 (mm) cc_final: 0.8775 (mt) REVERT: D 110 ARG cc_start: 0.5510 (mtt180) cc_final: 0.2958 (ptt-90) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 0.1436 time to fit residues: 16.0781 Evaluate side-chains 76 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.180729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.141673 restraints weight = 6004.344| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.17 r_work: 0.3366 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5701 Z= 0.147 Angle : 0.510 7.698 7766 Z= 0.260 Chirality : 0.040 0.145 886 Planarity : 0.004 0.043 936 Dihedral : 6.430 58.827 965 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.57 % Allowed : 9.42 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.34), residues: 665 helix: 1.77 (0.30), residues: 304 sheet: -1.26 (0.44), residues: 147 loop : -0.89 (0.44), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 232 HIS 0.003 0.001 HIS A 132 PHE 0.015 0.001 PHE A 286 TYR 0.016 0.001 TYR D 50 ARG 0.002 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.04330 ( 302) hydrogen bonds : angle 4.32910 ( 888) SS BOND : bond 0.00168 ( 4) SS BOND : angle 1.24591 ( 8) covalent geometry : bond 0.00335 ( 5697) covalent geometry : angle 0.50852 ( 7758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.581 Fit side-chains REVERT: A 168 ASN cc_start: 0.8296 (m-40) cc_final: 0.8014 (m-40) REVERT: A 216 THR cc_start: 0.7925 (m) cc_final: 0.7688 (m) REVERT: A 237 ASP cc_start: 0.7009 (m-30) cc_final: 0.6688 (m-30) REVERT: A 283 MET cc_start: 0.7877 (tpp) cc_final: 0.7516 (tpt) REVERT: D 77 SER cc_start: 0.7830 (m) cc_final: 0.7306 (p) REVERT: D 110 ARG cc_start: 0.5485 (mtt180) cc_final: 0.2920 (ptt-90) outliers start: 15 outliers final: 12 residues processed: 80 average time/residue: 0.1374 time to fit residues: 15.4161 Evaluate side-chains 79 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 10 optimal weight: 4.9990 chunk 57 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 55 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A1295 ASN D 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.180958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141946 restraints weight = 6014.421| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.17 r_work: 0.3321 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5701 Z= 0.133 Angle : 0.493 6.295 7766 Z= 0.251 Chirality : 0.039 0.143 886 Planarity : 0.004 0.045 936 Dihedral : 6.354 58.367 964 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.91 % Allowed : 10.10 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.34), residues: 665 helix: 1.87 (0.30), residues: 304 sheet: -1.16 (0.43), residues: 145 loop : -0.87 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.003 0.001 HIS A 132 PHE 0.014 0.001 PHE A 286 TYR 0.014 0.001 TYR D 50 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 302) hydrogen bonds : angle 4.14078 ( 888) SS BOND : bond 0.00161 ( 4) SS BOND : angle 1.16367 ( 8) covalent geometry : bond 0.00299 ( 5697) covalent geometry : angle 0.49134 ( 7758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.575 Fit side-chains REVERT: A 100 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7152 (mp) REVERT: A 168 ASN cc_start: 0.8272 (m-40) cc_final: 0.7916 (m-40) REVERT: A 200 ASN cc_start: 0.8011 (m-40) cc_final: 0.7754 (m-40) REVERT: A 216 THR cc_start: 0.7848 (m) cc_final: 0.7604 (m) REVERT: A 237 ASP cc_start: 0.6915 (m-30) cc_final: 0.6587 (m-30) REVERT: A 283 MET cc_start: 0.7828 (tpp) cc_final: 0.7456 (tpt) REVERT: A 1293 PHE cc_start: 0.7623 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: D 77 SER cc_start: 0.7789 (m) cc_final: 0.7227 (p) REVERT: D 110 ARG cc_start: 0.5525 (mtt180) cc_final: 0.2903 (ptt-90) outliers start: 17 outliers final: 13 residues processed: 81 average time/residue: 0.1372 time to fit residues: 15.6337 Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS D 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.181422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.142683 restraints weight = 5962.249| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.15 r_work: 0.3334 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5701 Z= 0.121 Angle : 0.476 5.622 7766 Z= 0.243 Chirality : 0.039 0.143 886 Planarity : 0.004 0.046 936 Dihedral : 6.094 57.898 960 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.74 % Allowed : 11.47 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.34), residues: 665 helix: 1.96 (0.30), residues: 304 sheet: -1.07 (0.43), residues: 145 loop : -0.78 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.013 0.001 PHE A 286 TYR 0.013 0.001 TYR D 50 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 302) hydrogen bonds : angle 4.02210 ( 888) SS BOND : bond 0.00164 ( 4) SS BOND : angle 1.10755 ( 8) covalent geometry : bond 0.00270 ( 5697) covalent geometry : angle 0.47511 ( 7758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.621 Fit side-chains REVERT: A 100 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7166 (mp) REVERT: A 168 ASN cc_start: 0.8272 (m-40) cc_final: 0.7929 (m-40) REVERT: A 200 ASN cc_start: 0.8037 (m-40) cc_final: 0.7674 (m-40) REVERT: A 216 THR cc_start: 0.7835 (m) cc_final: 0.7582 (m) REVERT: A 237 ASP cc_start: 0.6878 (m-30) cc_final: 0.6546 (m-30) REVERT: A 283 MET cc_start: 0.7822 (tpp) cc_final: 0.7482 (tpt) REVERT: A 1243 MET cc_start: 0.7901 (tpt) cc_final: 0.7427 (ttm) REVERT: A 1293 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6629 (m-80) REVERT: D 77 SER cc_start: 0.7793 (m) cc_final: 0.7234 (p) REVERT: D 110 ARG cc_start: 0.5499 (mtt180) cc_final: 0.2853 (ptt-90) outliers start: 16 outliers final: 11 residues processed: 79 average time/residue: 0.1558 time to fit residues: 16.9654 Evaluate side-chains 83 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.0370 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.181295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.142451 restraints weight = 5954.198| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.16 r_work: 0.3383 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5701 Z= 0.125 Angle : 0.491 9.057 7766 Z= 0.246 Chirality : 0.039 0.142 886 Planarity : 0.004 0.046 936 Dihedral : 6.090 57.964 959 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.08 % Allowed : 11.64 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.34), residues: 665 helix: 1.94 (0.30), residues: 305 sheet: -1.06 (0.43), residues: 145 loop : -0.85 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.014 0.001 PHE A 286 TYR 0.013 0.001 TYR D 50 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03916 ( 302) hydrogen bonds : angle 3.98651 ( 888) SS BOND : bond 0.00170 ( 4) SS BOND : angle 1.13770 ( 8) covalent geometry : bond 0.00280 ( 5697) covalent geometry : angle 0.49003 ( 7758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.589 Fit side-chains REVERT: A 51 ILE cc_start: 0.7900 (mt) cc_final: 0.7356 (mp) REVERT: A 55 PHE cc_start: 0.7483 (m-10) cc_final: 0.7110 (m-10) REVERT: A 100 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7207 (mp) REVERT: A 237 ASP cc_start: 0.6998 (m-30) cc_final: 0.6668 (m-30) REVERT: A 283 MET cc_start: 0.7862 (tpp) cc_final: 0.7526 (tpt) REVERT: A 1243 MET cc_start: 0.7968 (tpt) cc_final: 0.7520 (ttm) REVERT: A 1293 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.6677 (m-80) REVERT: D 5 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7576 (mmt) REVERT: D 77 SER cc_start: 0.7828 (m) cc_final: 0.7267 (p) REVERT: D 110 ARG cc_start: 0.5521 (mtt180) cc_final: 0.2933 (ptt-90) outliers start: 18 outliers final: 13 residues processed: 77 average time/residue: 0.1616 time to fit residues: 16.8775 Evaluate side-chains 81 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.179827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140777 restraints weight = 5946.317| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.15 r_work: 0.3311 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5701 Z= 0.153 Angle : 0.498 5.106 7766 Z= 0.255 Chirality : 0.040 0.140 886 Planarity : 0.004 0.045 936 Dihedral : 6.213 57.904 959 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.77 % Allowed : 10.96 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.34), residues: 665 helix: 1.84 (0.30), residues: 305 sheet: -1.09 (0.42), residues: 145 loop : -0.89 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.015 0.001 PHE A 286 TYR 0.016 0.001 TYR D 50 ARG 0.001 0.000 ARG A 126 Details of bonding type rmsd hydrogen bonds : bond 0.04128 ( 302) hydrogen bonds : angle 4.06581 ( 888) SS BOND : bond 0.00196 ( 4) SS BOND : angle 1.27479 ( 8) covalent geometry : bond 0.00352 ( 5697) covalent geometry : angle 0.49634 ( 7758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.532 Fit side-chains REVERT: A 55 PHE cc_start: 0.7491 (m-10) cc_final: 0.7102 (m-10) REVERT: A 100 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7259 (mp) REVERT: A 168 ASN cc_start: 0.8247 (m-40) cc_final: 0.7881 (m-40) REVERT: A 216 THR cc_start: 0.7974 (m) cc_final: 0.7702 (m) REVERT: A 237 ASP cc_start: 0.7044 (m-30) cc_final: 0.6705 (m-30) REVERT: A 283 MET cc_start: 0.7860 (tpp) cc_final: 0.7524 (tpt) REVERT: A 1243 MET cc_start: 0.7975 (tpt) cc_final: 0.7535 (ttm) REVERT: A 1293 PHE cc_start: 0.7662 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: D 5 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7514 (mmt) REVERT: D 77 SER cc_start: 0.7803 (m) cc_final: 0.7221 (p) REVERT: D 110 ARG cc_start: 0.5548 (mtt180) cc_final: 0.2930 (ptt-90) outliers start: 22 outliers final: 17 residues processed: 83 average time/residue: 0.1601 time to fit residues: 18.2287 Evaluate side-chains 89 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS D 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.180655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141589 restraints weight = 5956.531| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.16 r_work: 0.3323 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5701 Z= 0.131 Angle : 0.480 5.045 7766 Z= 0.246 Chirality : 0.039 0.141 886 Planarity : 0.004 0.046 936 Dihedral : 6.174 58.230 959 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.11 % Allowed : 11.13 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.34), residues: 665 helix: 1.92 (0.30), residues: 305 sheet: -1.02 (0.42), residues: 145 loop : -0.88 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.004 0.001 HIS A 132 PHE 0.014 0.001 PHE A 286 TYR 0.014 0.001 TYR D 50 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 302) hydrogen bonds : angle 3.99831 ( 888) SS BOND : bond 0.00189 ( 4) SS BOND : angle 1.16766 ( 8) covalent geometry : bond 0.00296 ( 5697) covalent geometry : angle 0.47897 ( 7758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.630 Fit side-chains REVERT: A 51 ILE cc_start: 0.7878 (mt) cc_final: 0.7340 (mp) REVERT: A 55 PHE cc_start: 0.7495 (m-10) cc_final: 0.7117 (m-10) REVERT: A 100 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7216 (mp) REVERT: A 102 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7523 (ptpt) REVERT: A 237 ASP cc_start: 0.6999 (m-30) cc_final: 0.6659 (m-30) REVERT: A 283 MET cc_start: 0.7852 (tpp) cc_final: 0.7517 (tpt) REVERT: A 1243 MET cc_start: 0.7961 (tpt) cc_final: 0.7536 (ttm) REVERT: A 1293 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: D 5 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7599 (mmt) REVERT: D 77 SER cc_start: 0.7798 (m) cc_final: 0.7213 (p) REVERT: D 110 ARG cc_start: 0.5574 (mtt180) cc_final: 0.2935 (ptt-90) outliers start: 24 outliers final: 17 residues processed: 80 average time/residue: 0.1977 time to fit residues: 21.8640 Evaluate side-chains 86 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 65 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 132 HIS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 296 GLN D 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.179616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140730 restraints weight = 6044.958| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.15 r_work: 0.3250 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5701 Z= 0.157 Angle : 0.498 5.106 7766 Z= 0.255 Chirality : 0.040 0.137 886 Planarity : 0.004 0.046 936 Dihedral : 6.219 58.175 959 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.60 % Allowed : 12.16 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.34), residues: 665 helix: 1.83 (0.30), residues: 305 sheet: -1.04 (0.43), residues: 145 loop : -0.89 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 232 HIS 0.008 0.001 HIS A 132 PHE 0.015 0.001 PHE A 286 TYR 0.016 0.001 TYR D 50 ARG 0.001 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 302) hydrogen bonds : angle 4.02716 ( 888) SS BOND : bond 0.00195 ( 4) SS BOND : angle 1.26960 ( 8) covalent geometry : bond 0.00363 ( 5697) covalent geometry : angle 0.49609 ( 7758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.546 Fit side-chains REVERT: A 51 ILE cc_start: 0.7830 (mt) cc_final: 0.7288 (mp) REVERT: A 55 PHE cc_start: 0.7475 (m-10) cc_final: 0.7089 (m-10) REVERT: A 100 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7219 (mp) REVERT: A 102 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7557 (ptpt) REVERT: A 168 ASN cc_start: 0.8217 (m-40) cc_final: 0.7868 (m-40) REVERT: A 200 ASN cc_start: 0.7965 (m-40) cc_final: 0.7758 (m-40) REVERT: A 237 ASP cc_start: 0.6992 (m-30) cc_final: 0.6648 (m-30) REVERT: A 283 MET cc_start: 0.7844 (tpp) cc_final: 0.7504 (tpt) REVERT: A 1243 MET cc_start: 0.7931 (tpt) cc_final: 0.7505 (ttm) REVERT: A 1293 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6658 (m-80) REVERT: D 5 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.7524 (mmt) REVERT: D 110 ARG cc_start: 0.5551 (mtt180) cc_final: 0.2897 (ptt-90) outliers start: 21 outliers final: 16 residues processed: 85 average time/residue: 0.1610 time to fit residues: 18.7857 Evaluate side-chains 91 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 1 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: A 132 HIS A 296 GLN D 102 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.180078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141227 restraints weight = 5995.783| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.15 r_work: 0.3258 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5701 Z= 0.140 Angle : 0.485 5.057 7766 Z= 0.249 Chirality : 0.039 0.140 886 Planarity : 0.004 0.046 936 Dihedral : 6.197 58.726 959 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.77 % Allowed : 11.82 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.34), residues: 665 helix: 1.89 (0.30), residues: 305 sheet: -1.01 (0.43), residues: 145 loop : -0.83 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 232 HIS 0.002 0.001 HIS A1256 PHE 0.014 0.001 PHE A 286 TYR 0.014 0.001 TYR D 50 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04025 ( 302) hydrogen bonds : angle 4.02093 ( 888) SS BOND : bond 0.00196 ( 4) SS BOND : angle 1.21383 ( 8) covalent geometry : bond 0.00319 ( 5697) covalent geometry : angle 0.48387 ( 7758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1330 Ramachandran restraints generated. 665 Oldfield, 0 Emsley, 665 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.544 Fit side-chains REVERT: A 51 ILE cc_start: 0.7844 (mt) cc_final: 0.7311 (mp) REVERT: A 55 PHE cc_start: 0.7470 (m-10) cc_final: 0.7093 (m-10) REVERT: A 100 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7211 (mp) REVERT: A 102 LYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7510 (ptpt) REVERT: A 168 ASN cc_start: 0.8247 (m-40) cc_final: 0.7902 (m-40) REVERT: A 200 ASN cc_start: 0.7960 (m-40) cc_final: 0.7747 (m-40) REVERT: A 237 ASP cc_start: 0.6962 (m-30) cc_final: 0.6616 (m-30) REVERT: A 283 MET cc_start: 0.7860 (tpp) cc_final: 0.7511 (tpt) REVERT: A 1243 MET cc_start: 0.7937 (tpt) cc_final: 0.7514 (ttm) REVERT: A 1293 PHE cc_start: 0.7613 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: D 5 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.7589 (mmt) REVERT: D 110 ARG cc_start: 0.5519 (mtt180) cc_final: 0.2874 (ptt-90) outliers start: 22 outliers final: 16 residues processed: 86 average time/residue: 0.1558 time to fit residues: 18.2052 Evaluate side-chains 91 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 327 ILE Chi-restraints excluded: chain A residue 341 LEU Chi-restraints excluded: chain A residue 1293 PHE Chi-restraints excluded: chain B residue 44 ARG Chi-restraints excluded: chain C residue 53 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 5 MET Chi-restraints excluded: chain D residue 66 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.0020 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS D 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.180516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.141835 restraints weight = 6042.115| |-----------------------------------------------------------------------------| r_work (start): 0.3626 rms_B_bonded: 2.16 r_work: 0.3387 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5701 Z= 0.127 Angle : 0.477 5.050 7766 Z= 0.245 Chirality : 0.039 0.141 886 Planarity : 0.003 0.046 936 Dihedral : 6.171 59.433 959 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.25 % Allowed : 12.84 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.34), residues: 665 helix: 1.97 (0.30), residues: 304 sheet: -0.94 (0.43), residues: 143 loop : -0.90 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 232 HIS 0.007 0.001 HIS A 132 PHE 0.014 0.001 PHE A 286 TYR 0.013 0.001 TYR D 50 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 302) hydrogen bonds : angle 3.94437 ( 888) SS BOND : bond 0.00180 ( 4) SS BOND : angle 1.15516 ( 8) covalent geometry : bond 0.00286 ( 5697) covalent geometry : angle 0.47598 ( 7758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3854.08 seconds wall clock time: 67 minutes 18.86 seconds (4038.86 seconds total)