Starting phenix.real_space_refine on Fri May 9 14:17:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k5d_36902/05_2025/8k5d_36902.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k5d_36902/05_2025/8k5d_36902.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k5d_36902/05_2025/8k5d_36902.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k5d_36902/05_2025/8k5d_36902.map" model { file = "/net/cci-nas-00/data/ceres_data/8k5d_36902/05_2025/8k5d_36902.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k5d_36902/05_2025/8k5d_36902.cif" } resolution = 3.74 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= -0.001 sd= 0.031 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 17 5.16 5 Cl 1 4.86 5 C 1561 2.51 5 N 394 2.21 5 O 372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 2345 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2328 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'OKL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.19, per 1000 atoms: 0.93 Number of scatterers: 2345 At special positions: 0 Unit cell: (69.72, 62.25, 79.68, 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 17 16.00 O 372 8.00 N 394 7.00 C 1561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " 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: 0.76 Conformation dependent library (CDL) restraints added in 325.4 milliseconds 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 558 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 2 sheets defined 75.9% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 29 through 54 removed outlier: 4.068A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 89 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 97 through 130 Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 140 through 166 removed outlier: 5.124A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.816A pdb=" N ALA A 191 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 223 through 260 removed outlier: 3.717A pdb=" N LYS A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.597A pdb=" N ARG A 270 " --> pdb=" O CYS A 266 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 272 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 278 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 283 " --> pdb=" O THR A 279 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR A 284 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N MET A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASN A 286 " --> pdb=" O PHE A 282 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER A 287 " --> pdb=" O THR A 283 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 165 hydrogen bonds defined for protein. 483 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.62 Time building geometry restraints manager: 0.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 713 1.34 - 1.46: 438 1.46 - 1.58: 1236 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 2413 Sorted by residual: bond pdb=" C07 OKL A 401 " pdb=" O08 OKL A 401 " ideal model delta sigma weight residual 1.214 1.398 -0.184 2.00e-02 2.50e+03 8.47e+01 bond pdb=" C10 OKL A 401 " pdb=" O11 OKL A 401 " ideal model delta sigma weight residual 1.215 1.396 -0.181 2.00e-02 2.50e+03 8.20e+01 bond pdb=" C15 OKL A 401 " pdb="CL17 OKL A 401 " ideal model delta sigma weight residual 1.692 1.784 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.390 1.325 0.065 2.00e-02 2.50e+03 1.07e+01 bond pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 1.384 1.328 0.056 2.00e-02 2.50e+03 7.72e+00 ... (remaining 2408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.90: 3204 1.90 - 3.81: 50 3.81 - 5.71: 22 5.71 - 7.62: 4 7.62 - 9.52: 4 Bond angle restraints: 3284 Sorted by residual: angle pdb=" N VAL A 27 " pdb=" CA VAL A 27 " pdb=" C VAL A 27 " ideal model delta sigma weight residual 111.91 108.72 3.19 8.90e-01 1.26e+00 1.28e+01 angle pdb=" N PRO A 31 " pdb=" CA PRO A 31 " pdb=" C PRO A 31 " ideal model delta sigma weight residual 110.70 114.65 -3.95 1.22e+00 6.72e-01 1.05e+01 angle pdb=" CA PRO A 31 " pdb=" C PRO A 31 " pdb=" N PRO A 32 " ideal model delta sigma weight residual 117.93 121.72 -3.79 1.20e+00 6.94e-01 9.98e+00 angle pdb=" C07 OKL A 401 " pdb=" N09 OKL A 401 " pdb=" C10 OKL A 401 " ideal model delta sigma weight residual 129.77 120.31 9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" C12 OKL A 401 " pdb=" C10 OKL A 401 " pdb=" N09 OKL A 401 " ideal model delta sigma weight residual 109.84 119.23 -9.39 3.00e+00 1.11e-01 9.80e+00 ... (remaining 3279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.19: 1261 27.19 - 54.38: 120 54.38 - 81.58: 7 81.58 - 108.77: 0 108.77 - 135.96: 1 Dihedral angle restraints: 1389 sinusoidal: 535 harmonic: 854 Sorted by residual: dihedral pdb=" C03 OKL A 401 " pdb=" C04 OKL A 401 " pdb=" C05 OKL A 401 " pdb=" N06 OKL A 401 " ideal model delta sinusoidal sigma weight residual 183.45 47.49 135.96 1 3.00e+01 1.11e-03 1.83e+01 dihedral pdb=" CA LYS A 164 " pdb=" C LYS A 164 " pdb=" N LYS A 165 " pdb=" CA LYS A 165 " ideal model delta harmonic sigma weight residual -180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" CA GLU A 196 " pdb=" C GLU A 196 " pdb=" N PHE A 197 " pdb=" CA PHE A 197 " ideal model delta harmonic sigma weight residual 180.00 163.64 16.36 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 1386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 261 0.037 - 0.074: 82 0.074 - 0.110: 28 0.110 - 0.147: 4 0.147 - 0.184: 3 Chirality restraints: 378 Sorted by residual: chirality pdb=" CA ASN A 110 " pdb=" N ASN A 110 " pdb=" C ASN A 110 " pdb=" CB ASN A 110 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA PRO A 31 " pdb=" N PRO A 31 " pdb=" C PRO A 31 " pdb=" CB PRO A 31 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA THR A 159 " pdb=" N THR A 159 " pdb=" C THR A 159 " pdb=" CB THR A 159 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 375 not shown) Planarity restraints: 398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 167 " 0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 168 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 168 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 168 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 31 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A 32 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 32 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 32 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 131 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 132 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 132 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 132 " 0.022 5.00e-02 4.00e+02 ... (remaining 395 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 258 2.74 - 3.28: 2460 3.28 - 3.82: 3903 3.82 - 4.36: 4195 4.36 - 4.90: 7307 Nonbonded interactions: 18123 Sorted by model distance: nonbonded pdb=" O ILE A 278 " pdb=" OG SER A 281 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASN A 68 " pdb=" NE1 TRP A 152 " model vdw 2.322 3.120 nonbonded pdb=" N SER A 179 " pdb=" O08 OKL A 401 " model vdw 2.326 3.120 nonbonded pdb=" NH2 ARG A 111 " pdb=" O11 OKL A 401 " model vdw 2.330 3.120 nonbonded pdb=" N ASP A 221 " pdb=" OD1 ASP A 221 " model vdw 2.345 3.120 ... (remaining 18118 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 0.410 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.820 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 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 : 0.007 0.184 2415 Z= 0.332 Angle : 0.755 9.520 3288 Z= 0.371 Chirality : 0.043 0.184 378 Planarity : 0.005 0.045 398 Dihedral : 19.082 135.960 825 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 0.40 % Allowed : 41.70 % Favored : 57.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.51), residues: 289 helix: 1.39 (0.37), residues: 202 sheet: None (None), residues: 0 loop : -2.40 (0.68), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 93 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.005 0.001 TYR A 126 ARG 0.002 0.000 ARG A 22 Details of bonding type rmsd hydrogen bonds : bond 0.12440 ( 165) hydrogen bonds : angle 5.08309 ( 483) SS BOND : bond 0.00159 ( 2) SS BOND : angle 0.34041 ( 4) covalent geometry : bond 0.00673 ( 2413) covalent geometry : angle 0.75568 ( 3284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.4006 (OUTLIER) cc_final: 0.3713 (m-10) REVERT: A 103 MET cc_start: 0.7450 (tpp) cc_final: 0.7040 (tpp) REVERT: A 170 GLN cc_start: 0.8195 (tp40) cc_final: 0.7866 (tp40) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.0922 time to fit residues: 8.1002 Evaluate side-chains 68 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 0.1980 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.151793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.134649 restraints weight = 3886.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.137825 restraints weight = 2281.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139927 restraints weight = 1553.127| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2415 Z= 0.127 Angle : 0.574 7.455 3288 Z= 0.298 Chirality : 0.040 0.130 378 Planarity : 0.005 0.049 398 Dihedral : 9.546 141.589 319 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.26 % Allowed : 34.41 % Favored : 60.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.50), residues: 289 helix: 1.25 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.68 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.011 0.001 PHE A 197 TYR 0.007 0.001 TYR A 284 ARG 0.001 0.000 ARG A 218 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 165) hydrogen bonds : angle 4.17091 ( 483) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.17920 ( 4) covalent geometry : bond 0.00284 ( 2413) covalent geometry : angle 0.57473 ( 3284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.266 Fit side-chains revert: symmetry clash REVERT: A 290 ASP cc_start: 0.8574 (m-30) cc_final: 0.8283 (m-30) outliers start: 13 outliers final: 11 residues processed: 75 average time/residue: 0.0930 time to fit residues: 8.8711 Evaluate side-chains 78 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.135110 restraints weight = 3898.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138340 restraints weight = 2352.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140438 restraints weight = 1636.226| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2415 Z= 0.163 Angle : 0.602 8.017 3288 Z= 0.309 Chirality : 0.041 0.133 378 Planarity : 0.005 0.049 398 Dihedral : 9.213 142.813 317 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 8.10 % Allowed : 32.39 % Favored : 59.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.51), residues: 289 helix: 1.35 (0.36), residues: 213 sheet: None (None), residues: 0 loop : -2.67 (0.68), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.010 0.002 TYR A 87 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 165) hydrogen bonds : angle 4.17988 ( 483) SS BOND : bond 0.00208 ( 2) SS BOND : angle 0.23685 ( 4) covalent geometry : bond 0.00389 ( 2413) covalent geometry : angle 0.60212 ( 3284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 68 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 87 TYR cc_start: 0.8536 (m-80) cc_final: 0.8324 (m-80) REVERT: A 290 ASP cc_start: 0.8665 (m-30) cc_final: 0.8195 (m-30) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.1045 time to fit residues: 10.0933 Evaluate side-chains 81 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.152304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.134902 restraints weight = 3838.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.138089 restraints weight = 2326.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.140175 restraints weight = 1606.218| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2415 Z= 0.157 Angle : 0.611 6.913 3288 Z= 0.311 Chirality : 0.040 0.126 378 Planarity : 0.005 0.048 398 Dihedral : 9.227 143.070 317 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 7.69 % Allowed : 32.79 % Favored : 59.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.51), residues: 289 helix: 1.43 (0.36), residues: 212 sheet: None (None), residues: 0 loop : -2.72 (0.67), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.009 0.002 TYR A 87 ARG 0.001 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 165) hydrogen bonds : angle 4.10855 ( 483) SS BOND : bond 0.00263 ( 2) SS BOND : angle 0.20949 ( 4) covalent geometry : bond 0.00376 ( 2413) covalent geometry : angle 0.61179 ( 3284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3947 (OUTLIER) cc_final: 0.3720 (m-10) REVERT: A 87 TYR cc_start: 0.8552 (m-80) cc_final: 0.8271 (m-80) REVERT: A 290 ASP cc_start: 0.8699 (m-30) cc_final: 0.8071 (m-30) outliers start: 19 outliers final: 14 residues processed: 74 average time/residue: 0.1006 time to fit residues: 9.1939 Evaluate side-chains 80 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 65 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 26 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.135262 restraints weight = 3942.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138407 restraints weight = 2340.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.140714 restraints weight = 1614.673| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2415 Z= 0.137 Angle : 0.595 8.648 3288 Z= 0.302 Chirality : 0.040 0.145 378 Planarity : 0.005 0.048 398 Dihedral : 9.128 141.737 317 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 8.10 % Allowed : 33.60 % Favored : 58.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.51), residues: 289 helix: 1.41 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.58 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 93 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.007 0.001 TYR A 284 ARG 0.001 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 165) hydrogen bonds : angle 4.03519 ( 483) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.22704 ( 4) covalent geometry : bond 0.00322 ( 2413) covalent geometry : angle 0.59534 ( 3284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 69 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3849 (OUTLIER) cc_final: 0.3619 (m-10) REVERT: A 63 ARG cc_start: 0.8462 (ttp-110) cc_final: 0.8179 (ttm-80) REVERT: A 110 ASN cc_start: 0.8665 (m-40) cc_final: 0.8445 (m110) REVERT: A 290 ASP cc_start: 0.8711 (m-30) cc_final: 0.8413 (m-30) outliers start: 20 outliers final: 18 residues processed: 78 average time/residue: 0.1010 time to fit residues: 9.7634 Evaluate side-chains 87 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.134432 restraints weight = 3849.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.137406 restraints weight = 2334.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.139624 restraints weight = 1636.369| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2415 Z= 0.155 Angle : 0.606 7.538 3288 Z= 0.314 Chirality : 0.041 0.156 378 Planarity : 0.005 0.049 398 Dihedral : 9.187 142.618 317 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 9.72 % Allowed : 31.58 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.51), residues: 289 helix: 1.37 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.63 (0.68), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.009 0.001 PHE A 197 TYR 0.008 0.001 TYR A 126 ARG 0.001 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 165) hydrogen bonds : angle 4.06006 ( 483) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.30347 ( 4) covalent geometry : bond 0.00370 ( 2413) covalent geometry : angle 0.60677 ( 3284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3897 (OUTLIER) cc_final: 0.3665 (m-10) REVERT: A 63 ARG cc_start: 0.8451 (ttp-110) cc_final: 0.8178 (ttm-80) REVERT: A 110 ASN cc_start: 0.8666 (m-40) cc_final: 0.8458 (m110) REVERT: A 290 ASP cc_start: 0.8725 (m-30) cc_final: 0.8377 (m-30) outliers start: 24 outliers final: 19 residues processed: 78 average time/residue: 0.1092 time to fit residues: 10.5847 Evaluate side-chains 86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 285 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.0470 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.152103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.134054 restraints weight = 3969.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137198 restraints weight = 2352.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.139475 restraints weight = 1631.947| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2415 Z= 0.139 Angle : 0.617 9.625 3288 Z= 0.310 Chirality : 0.041 0.135 378 Planarity : 0.005 0.049 398 Dihedral : 9.117 141.362 317 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 8.91 % Allowed : 32.39 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.51), residues: 289 helix: 1.43 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.67 (0.67), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.002 0.001 HIS A 161 PHE 0.010 0.001 PHE A 197 TYR 0.007 0.001 TYR A 126 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 165) hydrogen bonds : angle 4.03133 ( 483) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.17648 ( 4) covalent geometry : bond 0.00326 ( 2413) covalent geometry : angle 0.61736 ( 3284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 59 TRP cc_start: 0.3849 (OUTLIER) cc_final: 0.3563 (m-10) REVERT: A 290 ASP cc_start: 0.8741 (m-30) cc_final: 0.8341 (m-30) outliers start: 22 outliers final: 17 residues processed: 81 average time/residue: 0.1028 time to fit residues: 10.3153 Evaluate side-chains 85 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 165 LYS Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.0010 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.135493 restraints weight = 3991.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138639 restraints weight = 2349.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140981 restraints weight = 1621.053| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2415 Z= 0.126 Angle : 0.626 9.576 3288 Z= 0.310 Chirality : 0.040 0.164 378 Planarity : 0.005 0.049 398 Dihedral : 8.989 139.303 317 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.88 % Allowed : 34.01 % Favored : 59.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.51), residues: 289 helix: 1.49 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.71 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 152 HIS 0.002 0.000 HIS A 161 PHE 0.011 0.001 PHE A 197 TYR 0.005 0.001 TYR A 126 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 165) hydrogen bonds : angle 3.98371 ( 483) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.19467 ( 4) covalent geometry : bond 0.00286 ( 2413) covalent geometry : angle 0.62590 ( 3284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 67 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.8276 (m-40) cc_final: 0.7834 (m-40) REVERT: A 290 ASP cc_start: 0.8656 (m-30) cc_final: 0.8217 (m-30) outliers start: 17 outliers final: 15 residues processed: 76 average time/residue: 0.1070 time to fit residues: 10.1498 Evaluate side-chains 81 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 17 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.3980 chunk 19 optimal weight: 0.0770 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.154706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137113 restraints weight = 3853.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140192 restraints weight = 2290.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.142484 restraints weight = 1588.887| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2415 Z= 0.126 Angle : 0.620 9.105 3288 Z= 0.309 Chirality : 0.041 0.179 378 Planarity : 0.005 0.049 398 Dihedral : 8.926 138.278 317 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 6.07 % Allowed : 35.22 % Favored : 58.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.51), residues: 289 helix: 1.48 (0.36), residues: 214 sheet: None (None), residues: 0 loop : -2.74 (0.67), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 152 HIS 0.002 0.000 HIS A 161 PHE 0.011 0.001 PHE A 197 TYR 0.006 0.001 TYR A 126 ARG 0.002 0.000 ARG A 251 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 165) hydrogen bonds : angle 3.95468 ( 483) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.15637 ( 4) covalent geometry : bond 0.00285 ( 2413) covalent geometry : angle 0.62027 ( 3284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7862 (mt-10) REVERT: A 63 ARG cc_start: 0.8266 (ttm110) cc_final: 0.8003 (ttm110) REVERT: A 137 ASN cc_start: 0.8269 (m-40) cc_final: 0.7829 (m-40) REVERT: A 190 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8906 (mm-30) REVERT: A 290 ASP cc_start: 0.8644 (m-30) cc_final: 0.8182 (m-30) outliers start: 15 outliers final: 14 residues processed: 76 average time/residue: 0.1092 time to fit residues: 10.3470 Evaluate side-chains 80 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.152945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.135114 restraints weight = 3930.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.138324 restraints weight = 2331.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.140413 restraints weight = 1608.112| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2415 Z= 0.145 Angle : 0.638 8.875 3288 Z= 0.320 Chirality : 0.041 0.201 378 Planarity : 0.005 0.048 398 Dihedral : 9.057 140.430 317 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 6.48 % Allowed : 34.41 % Favored : 59.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.51), residues: 289 helix: 1.34 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.72 (0.67), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 152 HIS 0.001 0.000 HIS A 161 PHE 0.011 0.001 PHE A 197 TYR 0.008 0.001 TYR A 126 ARG 0.002 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 165) hydrogen bonds : angle 4.02124 ( 483) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.21801 ( 4) covalent geometry : bond 0.00341 ( 2413) covalent geometry : angle 0.63786 ( 3284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 578 Ramachandran restraints generated. 289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8226 (ttm110) cc_final: 0.7945 (ttm110) REVERT: A 137 ASN cc_start: 0.8317 (m-40) cc_final: 0.7816 (m-40) REVERT: A 190 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8919 (mm-30) REVERT: A 290 ASP cc_start: 0.8653 (m-30) cc_final: 0.8194 (m-30) outliers start: 16 outliers final: 14 residues processed: 77 average time/residue: 0.1079 time to fit residues: 10.2058 Evaluate side-chains 81 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 HIS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 100 CYS Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 29 random chunks: chunk 21 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.151677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133712 restraints weight = 3962.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136751 restraints weight = 2345.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.139102 restraints weight = 1627.351| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2415 Z= 0.162 Angle : 0.653 8.670 3288 Z= 0.329 Chirality : 0.042 0.192 378 Planarity : 0.005 0.048 398 Dihedral : 9.165 141.792 317 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 6.88 % Allowed : 33.20 % Favored : 59.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.51), residues: 289 helix: 1.23 (0.36), residues: 215 sheet: None (None), residues: 0 loop : -2.75 (0.66), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 152 HIS 0.002 0.001 HIS A 184 PHE 0.009 0.001 PHE A 197 TYR 0.009 0.001 TYR A 126 ARG 0.002 0.000 ARG A 63 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 165) hydrogen bonds : angle 4.09329 ( 483) SS BOND : bond 0.00274 ( 2) SS BOND : angle 0.30488 ( 4) covalent geometry : bond 0.00386 ( 2413) covalent geometry : angle 0.65305 ( 3284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1069.49 seconds wall clock time: 19 minutes 36.66 seconds (1176.66 seconds total)