Starting phenix.real_space_refine on Sun Apr 27 11:15:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eai_47832/04_2025/9eai_47832.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eai_47832/04_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_47832/04_2025/9eai_47832.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eai_47832/04_2025/9eai_47832.map" model { file = "/net/cci-nas-00/data/ceres_data/9eai_47832/04_2025/9eai_47832.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eai_47832/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 4.56, per 1000 atoms: 0.82 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: 1.43 Conformation dependent library (CDL) restraints added in 818.0 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: 0.73 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: 1.96 Time building geometry restraints manager: 1.66 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: 2.730 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: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.800 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.110 ------------------------------------------------------------------------------- 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 : 0.646 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: 0.1431 time to fit residues: 16.3884 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 : 0.575 ------------------------------------------------------------------------------- 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 = 0.141948 restraints weight = 5915.525| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.11 r_work: 0.3402 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 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 60.176 968 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 4.64221 ( 888) SS BOND : bond 0.00171 ( 4) SS BOND : angle 1.27374 ( 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 : 0.551 Fit side-chains REVERT: A 30 MET cc_start: 0.7447 (ttt) cc_final: 0.7220 (ptm) REVERT: A 168 ASN cc_start: 0.8091 (m-40) cc_final: 0.7822 (m-40) REVERT: A 200 ASN cc_start: 0.8086 (m-40) cc_final: 0.7804 (m-40) REVERT: A 216 THR cc_start: 0.8135 (m) cc_final: 0.7894 (m) REVERT: A 237 ASP cc_start: 0.7090 (m-30) cc_final: 0.6849 (m-30) REVERT: A 283 MET cc_start: 0.7987 (tpp) cc_final: 0.7684 (tpt) REVERT: D 49 ILE cc_start: 0.9084 (mm) cc_final: 0.8824 (mt) REVERT: D 110 ARG cc_start: 0.5599 (mtt180) cc_final: 0.3223 (ptt-90) outliers start: 12 outliers final: 10 residues processed: 80 average time/residue: 0.1505 time to fit residues: 16.8191 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 : 0.526 ------------------------------------------------------------------------------- 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: 0.9990 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4098 r_free = 0.4098 target = 0.180212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141247 restraints weight = 6013.176| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.15 r_work: 0.3356 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5701 Z= 0.164 Angle : 0.525 7.793 7766 Z= 0.267 Chirality : 0.040 0.145 886 Planarity : 0.004 0.043 936 Dihedral : 6.496 59.335 965 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.57 % Allowed : 9.93 % Favored : 87.50 % 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: 0.24 (0.34), residues: 665 helix: 1.70 (0.30), residues: 304 sheet: -1.29 (0.44), residues: 147 loop : -0.92 (0.44), residues: 214 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 0.015 0.001 PHE A 286 TYR 0.017 0.002 TYR D 50 ARG 0.001 0.000 ARG C 90 Details of bonding type rmsd hydrogen bonds : bond 0.04480 ( 302) hydrogen bonds : angle 4.40405 ( 888) SS BOND : bond 0.00174 ( 4) SS BOND : angle 1.31077 ( 8) covalent geometry : bond 0.00379 ( 5697) covalent geometry : angle 0.52325 ( 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 85 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.556 Fit side-chains REVERT: A 168 ASN cc_start: 0.8310 (m-40) cc_final: 0.7984 (m-40) REVERT: A 216 THR cc_start: 0.7956 (m) cc_final: 0.7712 (m) REVERT: A 237 ASP cc_start: 0.7049 (m-30) cc_final: 0.6719 (m-30) REVERT: A 283 MET cc_start: 0.7870 (tpp) cc_final: 0.7502 (tpt) REVERT: D 77 SER cc_start: 0.7838 (m) cc_final: 0.7303 (p) REVERT: D 110 ARG cc_start: 0.5472 (mtt180) cc_final: 0.2900 (ptt-90) outliers start: 15 outliers final: 11 residues processed: 81 average time/residue: 0.1375 time to fit residues: 15.7184 Evaluate side-chains 78 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0270 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 55 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.181863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.142910 restraints weight = 6000.432| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.16 r_work: 0.3336 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5701 Z= 0.115 Angle : 0.480 6.348 7766 Z= 0.245 Chirality : 0.038 0.144 886 Planarity : 0.004 0.045 936 Dihedral : 6.317 58.077 964 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.40 % Allowed : 10.62 % 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: 0.49 (0.34), residues: 665 helix: 1.92 (0.30), residues: 304 sheet: -1.15 (0.44), residues: 145 loop : -0.86 (0.44), residues: 216 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 0.013 0.001 PHE A 286 TYR 0.012 0.001 TYR C 63 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 302) hydrogen bonds : angle 4.11424 ( 888) SS BOND : bond 0.00159 ( 4) SS BOND : angle 1.09559 ( 8) covalent geometry : bond 0.00251 ( 5697) covalent geometry : angle 0.47925 ( 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 83 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.601 Fit side-chains REVERT: A 100 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7154 (mp) REVERT: A 168 ASN cc_start: 0.8217 (m-40) cc_final: 0.7930 (m-40) REVERT: A 200 ASN cc_start: 0.7993 (m-40) cc_final: 0.7738 (m-40) REVERT: A 216 THR cc_start: 0.7842 (m) cc_final: 0.7603 (m) REVERT: A 237 ASP cc_start: 0.6903 (m-30) cc_final: 0.6581 (m-30) REVERT: A 283 MET cc_start: 0.7836 (tpp) cc_final: 0.7468 (tpt) REVERT: A 1293 PHE cc_start: 0.7565 (OUTLIER) cc_final: 0.6590 (m-80) REVERT: D 77 SER cc_start: 0.7776 (m) cc_final: 0.7218 (p) REVERT: D 110 ARG cc_start: 0.5500 (mtt180) cc_final: 0.2884 (ptt-90) outliers start: 14 outliers final: 11 residues processed: 78 average time/residue: 0.1397 time to fit residues: 15.4696 Evaluate side-chains 81 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 60 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4097 r_free = 0.4097 target = 0.180304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.141383 restraints weight = 5981.206| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.16 r_work: 0.3365 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1241 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= 0.143 Angle : 0.496 5.670 7766 Z= 0.253 Chirality : 0.039 0.141 886 Planarity : 0.004 0.045 936 Dihedral : 6.171 58.311 960 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.08 % Allowed : 10.79 % Favored : 86.13 % 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: 0.45 (0.34), residues: 665 helix: 1.85 (0.30), residues: 304 sheet: -1.14 (0.43), residues: 145 loop : -0.83 (0.44), residues: 216 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 0.015 0.001 TYR D 50 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.04139 ( 302) hydrogen bonds : angle 4.10462 ( 888) SS BOND : bond 0.00177 ( 4) SS BOND : angle 1.22226 ( 8) covalent geometry : bond 0.00328 ( 5697) covalent geometry : angle 0.49432 ( 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 87 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.547 Fit side-chains REVERT: A 100 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7260 (mp) REVERT: A 168 ASN cc_start: 0.8335 (m-40) cc_final: 0.7971 (m-40) REVERT: A 200 ASN cc_start: 0.8058 (m-40) cc_final: 0.7705 (m-40) REVERT: A 237 ASP cc_start: 0.7037 (m-30) cc_final: 0.6707 (m-30) REVERT: A 283 MET cc_start: 0.7876 (tpp) cc_final: 0.7545 (tpt) REVERT: A 1293 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: D 77 SER cc_start: 0.7830 (m) cc_final: 0.7264 (p) REVERT: D 110 ARG cc_start: 0.5576 (mtt180) cc_final: 0.2922 (ptt-90) outliers start: 18 outliers final: 14 residues processed: 80 average time/residue: 0.1509 time to fit residues: 16.6244 Evaluate side-chains 85 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 69 time to evaluate : 0.531 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.0770 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 35 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.181952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143094 restraints weight = 5971.761| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.18 r_work: 0.3381 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5701 Z= 0.107 Angle : 0.461 5.112 7766 Z= 0.235 Chirality : 0.038 0.143 886 Planarity : 0.003 0.046 936 Dihedral : 6.019 58.481 959 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.08 % Allowed : 11.13 % 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: 0.64 (0.34), residues: 665 helix: 2.05 (0.30), residues: 305 sheet: -1.03 (0.43), residues: 145 loop : -0.81 (0.44), residues: 215 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 0.011 0.001 TYR D 50 ARG 0.002 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 302) hydrogen bonds : angle 3.93200 ( 888) SS BOND : bond 0.00159 ( 4) SS BOND : angle 1.04308 ( 8) covalent geometry : bond 0.00231 ( 5697) covalent geometry : angle 0.46007 ( 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 : 0.549 Fit side-chains REVERT: A 51 ILE cc_start: 0.8101 (mt) cc_final: 0.7567 (mp) REVERT: A 55 PHE cc_start: 0.7521 (m-10) cc_final: 0.7159 (m-10) REVERT: A 100 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7418 (mp) REVERT: A 237 ASP cc_start: 0.7031 (m-30) cc_final: 0.6772 (m-30) REVERT: A 283 MET cc_start: 0.7884 (tpp) cc_final: 0.7620 (tpt) REVERT: A 1243 MET cc_start: 0.7975 (tpt) cc_final: 0.7564 (ttm) REVERT: A 1293 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: D 77 SER cc_start: 0.7791 (m) cc_final: 0.7299 (p) REVERT: D 110 ARG cc_start: 0.5739 (mtt180) cc_final: 0.3262 (ptt-90) outliers start: 18 outliers final: 12 residues processed: 78 average time/residue: 0.1627 time to fit residues: 17.6213 Evaluate side-chains 79 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 64 optimal weight: 0.1980 chunk 57 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.181455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.143196 restraints weight = 5937.168| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.09 r_work: 0.3388 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1385 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= 0.129 Angle : 0.491 9.309 7766 Z= 0.246 Chirality : 0.039 0.140 886 Planarity : 0.004 0.047 936 Dihedral : 6.077 59.085 959 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.25 % Allowed : 11.64 % Favored : 85.10 % 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: 1.98 (0.30), residues: 305 sheet: -1.02 (0.43), residues: 145 loop : -0.84 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.03907 ( 302) hydrogen bonds : angle 3.95769 ( 888) SS BOND : bond 0.00179 ( 4) SS BOND : angle 1.16181 ( 8) covalent geometry : bond 0.00290 ( 5697) covalent geometry : angle 0.48977 ( 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 85 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.642 Fit side-chains REVERT: A 55 PHE cc_start: 0.7413 (m-10) cc_final: 0.7012 (m-10) REVERT: A 100 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7143 (mp) REVERT: A 237 ASP cc_start: 0.6963 (m-30) cc_final: 0.6625 (m-30) REVERT: A 283 MET cc_start: 0.7840 (tpp) cc_final: 0.7504 (tpt) REVERT: A 1243 MET cc_start: 0.7914 (tpt) cc_final: 0.7489 (ttm) REVERT: A 1293 PHE cc_start: 0.7583 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: D 5 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7563 (mmt) REVERT: D 77 SER cc_start: 0.7833 (m) cc_final: 0.7251 (p) REVERT: D 110 ARG cc_start: 0.5562 (mtt180) cc_final: 0.2936 (ptt-90) outliers start: 19 outliers final: 13 residues processed: 76 average time/residue: 0.1717 time to fit residues: 17.7487 Evaluate side-chains 82 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 66 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.180389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.141507 restraints weight = 5979.875| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.15 r_work: 0.3319 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5701 Z= 0.139 Angle : 0.484 5.063 7766 Z= 0.248 Chirality : 0.039 0.139 886 Planarity : 0.004 0.047 936 Dihedral : 6.158 59.264 959 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.77 % Allowed : 11.64 % Favored : 84.59 % 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: 0.55 (0.34), residues: 665 helix: 1.94 (0.30), residues: 305 sheet: -1.00 (0.43), residues: 145 loop : -0.86 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 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 0.03989 ( 302) hydrogen bonds : angle 3.99550 ( 888) SS BOND : bond 0.00194 ( 4) SS BOND : angle 1.20679 ( 8) covalent geometry : bond 0.00316 ( 5697) covalent geometry : angle 0.48319 ( 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 86 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.672 Fit side-chains REVERT: A 51 ILE cc_start: 0.7883 (mt) cc_final: 0.7353 (mp) REVERT: A 55 PHE cc_start: 0.7447 (m-10) cc_final: 0.7072 (m-10) REVERT: A 100 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7221 (mp) REVERT: A 237 ASP cc_start: 0.7027 (m-30) cc_final: 0.6690 (m-30) REVERT: A 283 MET cc_start: 0.7846 (tpp) cc_final: 0.7509 (tpt) REVERT: A 1243 MET cc_start: 0.7956 (tpt) cc_final: 0.7533 (ttm) REVERT: A 1293 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6686 (m-80) REVERT: D 5 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.7579 (mmt) REVERT: D 110 ARG cc_start: 0.5591 (mtt180) cc_final: 0.2952 (ptt-90) outliers start: 22 outliers final: 17 residues processed: 78 average time/residue: 0.1981 time to fit residues: 21.3227 Evaluate side-chains 84 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 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 212 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 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: 0.8980 chunk 15 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.0270 chunk 44 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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 = 0.4095 r_free = 0.4095 target = 0.180620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.141945 restraints weight = 6059.652| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.17 r_work: 0.3406 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.003 0.029 5701 Z= 0.127 Angle : 0.481 5.031 7766 Z= 0.245 Chirality : 0.039 0.141 886 Planarity : 0.004 0.047 936 Dihedral : 6.150 59.925 959 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.04 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: 0.60 (0.34), residues: 665 helix: 1.99 (0.30), residues: 305 sheet: -0.98 (0.43), residues: 145 loop : -0.84 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.008 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 0.03919 ( 302) hydrogen bonds : angle 3.93798 ( 888) SS BOND : bond 0.00182 ( 4) SS BOND : angle 1.16837 ( 8) covalent geometry : bond 0.00286 ( 5697) covalent geometry : angle 0.47968 ( 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 85 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.596 Fit side-chains REVERT: A 51 ILE cc_start: 0.8142 (mt) cc_final: 0.7613 (mp) REVERT: A 55 PHE cc_start: 0.7515 (m-10) cc_final: 0.7144 (m-10) REVERT: A 100 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7473 (mp) REVERT: A 237 ASP cc_start: 0.7116 (m-30) cc_final: 0.6859 (m-30) REVERT: A 283 MET cc_start: 0.7895 (tpp) cc_final: 0.7636 (tpt) REVERT: A 1243 MET cc_start: 0.8041 (tpt) cc_final: 0.7655 (ttm) REVERT: A 1293 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: D 5 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.7544 (mmt) REVERT: D 110 ARG cc_start: 0.5803 (mtt180) cc_final: 0.3312 (ptt-90) outliers start: 21 outliers final: 16 residues processed: 78 average time/residue: 0.1737 time to fit residues: 19.0989 Evaluate side-chains 83 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 41 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.0470 chunk 1 optimal weight: 1.9990 overall best weight: 0.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 ASN A 132 HIS A 296 GLN D 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.179092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140102 restraints weight = 5975.860| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.13 r_work: 0.3185 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5701 Z= 0.179 Angle : 0.518 5.247 7766 Z= 0.265 Chirality : 0.041 0.136 886 Planarity : 0.004 0.047 936 Dihedral : 6.299 58.531 959 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.25 % Allowed : 12.50 % 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: 0.40 (0.34), residues: 665 helix: 1.79 (0.29), residues: 305 sheet: -1.07 (0.43), residues: 145 loop : -0.89 (0.44), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 232 HIS 0.008 0.002 HIS A 132 PHE 0.015 0.001 PHE A 286 TYR 0.018 0.002 TYR D 50 ARG 0.002 0.000 ARG C 41 Details of bonding type rmsd hydrogen bonds : bond 0.04296 ( 302) hydrogen bonds : angle 4.11106 ( 888) SS BOND : bond 0.00210 ( 4) SS BOND : angle 1.36429 ( 8) covalent geometry : bond 0.00420 ( 5697) covalent geometry : angle 0.51630 ( 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 89 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 0.576 Fit side-chains REVERT: A 51 ILE cc_start: 0.7813 (mt) cc_final: 0.7279 (mp) REVERT: A 55 PHE cc_start: 0.7449 (m-10) cc_final: 0.7042 (m-10) REVERT: A 168 ASN cc_start: 0.8173 (m-40) cc_final: 0.7817 (m-40) REVERT: A 200 ASN cc_start: 0.7949 (m-40) cc_final: 0.7723 (m-40) REVERT: A 237 ASP cc_start: 0.6952 (m-30) cc_final: 0.6590 (m-30) REVERT: A 283 MET cc_start: 0.7834 (tpp) cc_final: 0.7489 (tpt) REVERT: A 1243 MET cc_start: 0.7928 (tpt) cc_final: 0.7492 (ttm) REVERT: A 1293 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: D 5 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7566 (mmt) REVERT: D 110 ARG cc_start: 0.5488 (mtt180) cc_final: 0.2847 (ptt-90) outliers start: 19 outliers final: 15 residues processed: 83 average time/residue: 0.1518 time to fit residues: 17.2224 Evaluate side-chains 86 residues out of total 584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR 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 31 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 21 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 chunk 52 optimal weight: 0.1980 chunk 35 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.182489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.143580 restraints weight = 6039.387| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.20 r_work: 0.3391 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5701 Z= 0.104 Angle : 0.457 4.966 7766 Z= 0.232 Chirality : 0.038 0.145 886 Planarity : 0.003 0.048 936 Dihedral : 6.038 57.828 959 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.91 % Allowed : 12.84 % 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: 0.76 (0.34), residues: 665 helix: 2.11 (0.30), residues: 305 sheet: -0.75 (0.43), residues: 142 loop : -0.87 (0.43), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 232 HIS 0.008 0.001 HIS A 132 PHE 0.013 0.001 PHE A 286 TYR 0.009 0.001 TYR D 50 ARG 0.001 0.000 ARG A 93 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 302) hydrogen bonds : angle 3.84982 ( 888) SS BOND : bond 0.00178 ( 4) SS BOND : angle 1.03649 ( 8) covalent geometry : bond 0.00223 ( 5697) covalent geometry : angle 0.45634 ( 7758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3807.50 seconds wall clock time: 66 minutes 54.65 seconds (4014.65 seconds total)