Starting phenix.real_space_refine on Wed Sep 17 03:19:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bgy_44526/09_2025/9bgy_44526.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bgy_44526/09_2025/9bgy_44526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bgy_44526/09_2025/9bgy_44526.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bgy_44526/09_2025/9bgy_44526.map" model { file = "/net/cci-nas-00/data/ceres_data/9bgy_44526/09_2025/9bgy_44526.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bgy_44526/09_2025/9bgy_44526.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 1931 2.51 5 N 456 2.21 5 O 509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2916 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2916 Classifications: {'peptide': 389} Link IDs: {'PTRANS': 16, 'TRANS': 372} Time building chain proxies: 1.11, per 1000 atoms: 0.38 Number of scatterers: 2916 At special positions: 0 Unit cell: (68.475, 61.875, 80.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 509 8.00 N 456 7.00 C 1931 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.29 Conformation dependent library (CDL) restraints added in 128.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 90.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 Processing helix chain 'A' and resid 23 through 27 removed outlier: 3.702A pdb=" N PHE A 27 " --> pdb=" O LYS A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 41 removed outlier: 3.838A pdb=" N GLY A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.786A pdb=" N GLY A 59 " --> pdb=" O ILE A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 93 removed outlier: 3.855A pdb=" N LEU A 64 " --> pdb=" O ASP A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 154 removed outlier: 3.581A pdb=" N GLY A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 180 removed outlier: 3.705A pdb=" N LYS A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 205 through 231 removed outlier: 3.761A pdb=" N TYR A 224 " --> pdb=" O ILE A 220 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 243 Processing helix chain 'A' and resid 243 through 254 Processing helix chain 'A' and resid 255 through 271 Proline residue: A 261 - end of helix Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.607A pdb=" N PHE A 279 " --> pdb=" O SER A 275 " (cutoff:3.500A) Proline residue: A 282 - end of helix removed outlier: 3.856A pdb=" N THR A 286 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.559A pdb=" N ILE A 301 " --> pdb=" O GLY A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 321 Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 329 through 333 removed outlier: 3.722A pdb=" N GLY A 332 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 351 through 361 removed outlier: 4.255A pdb=" N ILE A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 360 " --> pdb=" O ALA A 356 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 387 removed outlier: 3.509A pdb=" N LEU A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 699 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: 0.38 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 889 1.34 - 1.46: 598 1.46 - 1.58: 1444 1.58 - 1.69: 0 1.69 - 1.81: 37 Bond restraints: 2968 Sorted by residual: bond pdb=" N MET A 1 " pdb=" CA MET A 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" C ILE A 243 " pdb=" O ILE A 243 " ideal model delta sigma weight residual 1.236 1.228 0.008 1.19e-02 7.06e+03 4.82e-01 bond pdb=" CA ILE A 243 " pdb=" C ILE A 243 " ideal model delta sigma weight residual 1.523 1.531 -0.008 1.27e-02 6.20e+03 4.15e-01 bond pdb=" N VAL A 333 " pdb=" CA VAL A 333 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.22e-02 6.72e+03 3.54e-01 bond pdb=" CA ILE A 222 " pdb=" CB ILE A 222 " ideal model delta sigma weight residual 1.540 1.548 -0.008 1.36e-02 5.41e+03 3.37e-01 ... (remaining 2963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.93: 3834 0.93 - 1.86: 155 1.86 - 2.80: 20 2.80 - 3.73: 15 3.73 - 4.66: 9 Bond angle restraints: 4033 Sorted by residual: angle pdb=" N THR A 286 " pdb=" CA THR A 286 " pdb=" C THR A 286 " ideal model delta sigma weight residual 114.04 111.50 2.54 1.24e+00 6.50e-01 4.21e+00 angle pdb=" N ALA A 285 " pdb=" CA ALA A 285 " pdb=" C ALA A 285 " ideal model delta sigma weight residual 113.01 110.68 2.33 1.20e+00 6.94e-01 3.77e+00 angle pdb=" C LEU A 321 " pdb=" N THR A 322 " pdb=" CA THR A 322 " ideal model delta sigma weight residual 121.54 124.32 -2.78 1.91e+00 2.74e-01 2.12e+00 angle pdb=" CB ARG A 238 " pdb=" CG ARG A 238 " pdb=" CD ARG A 238 " ideal model delta sigma weight residual 111.30 114.53 -3.23 2.30e+00 1.89e-01 1.97e+00 angle pdb=" N ILE A 42 " pdb=" CA ILE A 42 " pdb=" CB ILE A 42 " ideal model delta sigma weight residual 112.07 109.95 2.12 1.52e+00 4.33e-01 1.95e+00 ... (remaining 4028 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.51: 1572 16.51 - 33.02: 145 33.02 - 49.53: 41 49.53 - 66.04: 8 66.04 - 82.55: 1 Dihedral angle restraints: 1767 sinusoidal: 662 harmonic: 1105 Sorted by residual: dihedral pdb=" CG ARG A 37 " pdb=" CD ARG A 37 " pdb=" NE ARG A 37 " pdb=" CZ ARG A 37 " ideal model delta sinusoidal sigma weight residual -90.00 -134.69 44.69 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CG ARG A 369 " pdb=" CD ARG A 369 " pdb=" NE ARG A 369 " pdb=" CZ ARG A 369 " ideal model delta sinusoidal sigma weight residual 180.00 -136.56 -43.44 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB MET A 289 " pdb=" CG MET A 289 " pdb=" SD MET A 289 " pdb=" CE MET A 289 " ideal model delta sinusoidal sigma weight residual 180.00 122.66 57.34 3 1.50e+01 4.44e-03 9.44e+00 ... (remaining 1764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 331 0.027 - 0.055: 107 0.055 - 0.082: 59 0.082 - 0.110: 14 0.110 - 0.137: 3 Chirality restraints: 514 Sorted by residual: chirality pdb=" CA ILE A 123 " pdb=" N ILE A 123 " pdb=" C ILE A 123 " pdb=" CB ILE A 123 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.72e-01 chirality pdb=" CA VAL A 272 " pdb=" N VAL A 272 " pdb=" C VAL A 272 " pdb=" CB VAL A 272 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA VAL A 333 " pdb=" N VAL A 333 " pdb=" C VAL A 333 " pdb=" CB VAL A 333 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.18e-01 ... (remaining 511 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 322 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C THR A 322 " 0.068 2.00e-02 2.50e+03 pdb=" O THR A 322 " -0.025 2.00e-02 2.50e+03 pdb=" N ALA A 323 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 27 " -0.007 2.00e-02 2.50e+03 9.33e-03 1.52e+00 pdb=" CG PHE A 27 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 27 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 27 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 27 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 27 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 27 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 272 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO A 273 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 273 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 273 " -0.015 5.00e-02 4.00e+02 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 51 2.70 - 3.25: 3207 3.25 - 3.80: 4819 3.80 - 4.35: 5919 4.35 - 4.90: 10177 Nonbonded interactions: 24173 Sorted by model distance: nonbonded pdb=" O LEU A 321 " pdb=" OG1 THR A 322 " model vdw 2.152 3.040 nonbonded pdb=" OD1 ASP A 366 " pdb=" NH2 ARG A 369 " model vdw 2.194 3.120 nonbonded pdb=" OH TYR A 224 " pdb=" OD2 ASP A 290 " model vdw 2.249 3.040 nonbonded pdb=" O LEU A 87 " pdb=" ND2 ASN A 91 " model vdw 2.463 3.120 nonbonded pdb=" O LEU A 46 " pdb=" OG1 THR A 50 " model vdw 2.474 3.040 ... (remaining 24168 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 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: 2.880 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.230 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 0.032 2968 Z= 0.130 Angle : 0.500 4.660 4033 Z= 0.269 Chirality : 0.036 0.137 514 Planarity : 0.003 0.039 488 Dihedral : 14.215 82.551 1059 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.32 % Allowed : 14.97 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.44), residues: 387 helix: 2.15 (0.28), residues: 335 sheet: None (None), residues: 0 loop : 0.71 (1.10), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 37 TYR 0.006 0.001 TYR A 184 PHE 0.021 0.001 PHE A 27 TRP 0.002 0.001 TRP A 192 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 2968) covalent geometry : angle 0.49955 ( 4033) hydrogen bonds : bond 0.11231 ( 235) hydrogen bonds : angle 5.18952 ( 699) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.089 Fit side-chains REVERT: A 24 LYS cc_start: 0.8310 (mttm) cc_final: 0.8009 (mttp) REVERT: A 26 GLU cc_start: 0.7418 (tp30) cc_final: 0.7150 (tp30) REVERT: A 61 VAL cc_start: 0.8326 (m) cc_final: 0.8088 (t) REVERT: A 62 LYS cc_start: 0.8402 (mttt) cc_final: 0.8132 (mtpm) REVERT: A 63 LYS cc_start: 0.8217 (tttt) cc_final: 0.7852 (tttm) REVERT: A 94 LYS cc_start: 0.7874 (mttt) cc_final: 0.7673 (mttp) REVERT: A 131 MET cc_start: 0.8474 (tpp) cc_final: 0.8170 (mmt) REVERT: A 158 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7442 (mm-30) REVERT: A 237 LEU cc_start: 0.8443 (tp) cc_final: 0.8176 (tm) REVERT: A 241 LYS cc_start: 0.8517 (ttmm) cc_final: 0.8235 (ttmt) REVERT: A 288 ASN cc_start: 0.8885 (t0) cc_final: 0.8657 (t0) REVERT: A 289 MET cc_start: 0.8199 (mmp) cc_final: 0.7768 (mmt) REVERT: A 325 LEU cc_start: 0.8048 (tm) cc_final: 0.7824 (mm) outliers start: 1 outliers final: 1 residues processed: 87 average time/residue: 0.5877 time to fit residues: 52.2864 Evaluate side-chains 75 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.4980 chunk 16 optimal weight: 0.0980 chunk 32 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.0170 chunk 30 optimal weight: 0.0570 chunk 22 optimal weight: 0.4980 chunk 37 optimal weight: 0.6980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 296 GLN A 305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.097156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.086205 restraints weight = 4758.603| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 1.60 r_work: 0.3069 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2968 Z= 0.130 Angle : 0.578 6.879 4033 Z= 0.284 Chirality : 0.040 0.129 514 Planarity : 0.004 0.035 488 Dihedral : 3.815 17.584 407 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.82 % Allowed : 17.83 % Favored : 78.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.90 (0.44), residues: 387 helix: 2.12 (0.28), residues: 340 sheet: None (None), residues: 0 loop : 0.57 (1.14), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 369 TYR 0.007 0.001 TYR A 4 PHE 0.011 0.001 PHE A 11 TRP 0.002 0.001 TRP A 192 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 2968) covalent geometry : angle 0.57782 ( 4033) hydrogen bonds : bond 0.03683 ( 235) hydrogen bonds : angle 4.56003 ( 699) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.093 Fit side-chains REVERT: A 26 GLU cc_start: 0.7815 (tp30) cc_final: 0.7418 (tp30) REVERT: A 61 VAL cc_start: 0.8578 (m) cc_final: 0.8308 (t) REVERT: A 63 LYS cc_start: 0.8503 (tttt) cc_final: 0.8287 (ttpt) REVERT: A 131 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8355 (mmt) REVERT: A 153 MET cc_start: 0.6182 (mtt) cc_final: 0.5777 (mtp) REVERT: A 237 LEU cc_start: 0.8742 (tp) cc_final: 0.8515 (tm) REVERT: A 312 THR cc_start: 0.8187 (p) cc_final: 0.7923 (p) REVERT: A 325 LEU cc_start: 0.8294 (tm) cc_final: 0.8052 (mm) outliers start: 12 outliers final: 4 residues processed: 85 average time/residue: 0.5785 time to fit residues: 50.3868 Evaluate side-chains 74 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 276 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.0670 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.0970 chunk 34 optimal weight: 0.5980 chunk 30 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 overall best weight: 0.1914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.099670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.088263 restraints weight = 4687.117| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.66 r_work: 0.3101 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2968 Z= 0.123 Angle : 0.569 6.024 4033 Z= 0.282 Chirality : 0.039 0.127 514 Planarity : 0.004 0.037 488 Dihedral : 3.926 19.554 407 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.14 % Allowed : 18.47 % Favored : 77.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.98 (0.44), residues: 387 helix: 2.18 (0.28), residues: 334 sheet: None (None), residues: 0 loop : 0.77 (1.03), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 386 TYR 0.008 0.001 TYR A 4 PHE 0.011 0.001 PHE A 11 TRP 0.001 0.000 TRP A 192 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 2968) covalent geometry : angle 0.56896 ( 4033) hydrogen bonds : bond 0.03426 ( 235) hydrogen bonds : angle 4.46929 ( 699) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.114 Fit side-chains REVERT: A 21 PHE cc_start: 0.8424 (m-10) cc_final: 0.8152 (m-10) REVERT: A 26 GLU cc_start: 0.7729 (tp30) cc_final: 0.7400 (tp30) REVERT: A 61 VAL cc_start: 0.8550 (m) cc_final: 0.8276 (t) REVERT: A 63 LYS cc_start: 0.8462 (tttt) cc_final: 0.8229 (ttpt) REVERT: A 131 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8363 (mmt) REVERT: A 153 MET cc_start: 0.6222 (mtt) cc_final: 0.5854 (mtp) REVERT: A 312 THR cc_start: 0.8190 (p) cc_final: 0.7938 (p) REVERT: A 325 LEU cc_start: 0.8307 (tm) cc_final: 0.8086 (mm) outliers start: 13 outliers final: 4 residues processed: 81 average time/residue: 0.5144 time to fit residues: 42.7896 Evaluate side-chains 76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 292 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 chunk 15 optimal weight: 0.0870 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.0060 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.098629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.087415 restraints weight = 4740.532| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.61 r_work: 0.3082 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2968 Z= 0.158 Angle : 0.568 6.148 4033 Z= 0.285 Chirality : 0.040 0.128 514 Planarity : 0.004 0.033 488 Dihedral : 3.962 18.418 405 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.50 % Allowed : 20.06 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.44), residues: 387 helix: 2.10 (0.28), residues: 334 sheet: None (None), residues: 0 loop : 0.78 (1.04), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 229 TYR 0.009 0.002 TYR A 307 PHE 0.015 0.002 PHE A 164 TRP 0.001 0.001 TRP A 192 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 2968) covalent geometry : angle 0.56777 ( 4033) hydrogen bonds : bond 0.03589 ( 235) hydrogen bonds : angle 4.53322 ( 699) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.121 Fit side-chains REVERT: A 26 GLU cc_start: 0.7809 (tp30) cc_final: 0.7436 (tp30) REVERT: A 29 LYS cc_start: 0.8381 (tttp) cc_final: 0.8180 (tttm) REVERT: A 61 VAL cc_start: 0.8615 (m) cc_final: 0.8309 (t) REVERT: A 131 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8379 (mmt) REVERT: A 153 MET cc_start: 0.6352 (mtt) cc_final: 0.5947 (mtp) REVERT: A 255 SER cc_start: 0.8858 (p) cc_final: 0.8536 (p) REVERT: A 312 THR cc_start: 0.8190 (p) cc_final: 0.7965 (p) REVERT: A 325 LEU cc_start: 0.8362 (tm) cc_final: 0.8107 (mm) outliers start: 11 outliers final: 4 residues processed: 78 average time/residue: 0.5417 time to fit residues: 43.3750 Evaluate side-chains 76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 111 ASN Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 292 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 20 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 33 optimal weight: 0.0570 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 ASN A 305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.085110 restraints weight = 4645.807| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 1.59 r_work: 0.3045 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2968 Z= 0.158 Angle : 0.575 6.250 4033 Z= 0.287 Chirality : 0.040 0.125 514 Planarity : 0.004 0.033 488 Dihedral : 4.023 18.520 405 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.46 % Allowed : 21.34 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.80 (0.44), residues: 387 helix: 2.10 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.45 (1.03), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 369 TYR 0.009 0.002 TYR A 307 PHE 0.014 0.002 PHE A 164 TRP 0.001 0.001 TRP A 192 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 2968) covalent geometry : angle 0.57531 ( 4033) hydrogen bonds : bond 0.03550 ( 235) hydrogen bonds : angle 4.58325 ( 699) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.111 Fit side-chains REVERT: A 26 GLU cc_start: 0.7807 (tp30) cc_final: 0.7405 (tp30) REVERT: A 29 LYS cc_start: 0.8405 (tttp) cc_final: 0.8199 (tttm) REVERT: A 61 VAL cc_start: 0.8611 (m) cc_final: 0.8302 (t) REVERT: A 131 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8328 (mmt) REVERT: A 153 MET cc_start: 0.6325 (mtt) cc_final: 0.5927 (mtp) REVERT: A 255 SER cc_start: 0.8886 (p) cc_final: 0.8563 (p) REVERT: A 312 THR cc_start: 0.8205 (p) cc_final: 0.7973 (p) REVERT: A 325 LEU cc_start: 0.8390 (tm) cc_final: 0.8128 (mm) outliers start: 14 outliers final: 5 residues processed: 83 average time/residue: 0.5169 time to fit residues: 44.0366 Evaluate side-chains 79 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 274 GLU Chi-restraints excluded: chain A residue 292 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 0.4980 chunk 6 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 30 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.098088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086962 restraints weight = 4721.629| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 1.59 r_work: 0.3068 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2968 Z= 0.188 Angle : 0.606 6.436 4033 Z= 0.301 Chirality : 0.041 0.130 514 Planarity : 0.004 0.032 488 Dihedral : 4.156 18.156 405 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.82 % Allowed : 21.97 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.67 (0.43), residues: 387 helix: 1.99 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.55 (1.02), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 369 TYR 0.011 0.002 TYR A 307 PHE 0.016 0.002 PHE A 164 TRP 0.001 0.001 TRP A 192 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 2968) covalent geometry : angle 0.60592 ( 4033) hydrogen bonds : bond 0.03696 ( 235) hydrogen bonds : angle 4.67362 ( 699) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.123 Fit side-chains REVERT: A 26 GLU cc_start: 0.7831 (tp30) cc_final: 0.7437 (tp30) REVERT: A 29 LYS cc_start: 0.8393 (tttp) cc_final: 0.8173 (tttm) REVERT: A 61 VAL cc_start: 0.8669 (m) cc_final: 0.8324 (t) REVERT: A 111 ASN cc_start: 0.7843 (p0) cc_final: 0.7617 (OUTLIER) REVERT: A 131 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8382 (mmt) REVERT: A 153 MET cc_start: 0.6397 (mtt) cc_final: 0.5998 (mtp) REVERT: A 211 THR cc_start: 0.8909 (t) cc_final: 0.8594 (p) REVERT: A 255 SER cc_start: 0.8841 (p) cc_final: 0.8516 (p) REVERT: A 312 THR cc_start: 0.8212 (p) cc_final: 0.7981 (p) REVERT: A 313 LEU cc_start: 0.8753 (tm) cc_final: 0.8394 (tt) REVERT: A 325 LEU cc_start: 0.8437 (tm) cc_final: 0.8185 (mm) outliers start: 12 outliers final: 5 residues processed: 78 average time/residue: 0.5473 time to fit residues: 43.8786 Evaluate side-chains 77 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 PHE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 292 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.1980 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 2 optimal weight: 0.0470 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 0.0980 chunk 8 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 overall best weight: 0.2078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.099935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.088695 restraints weight = 4693.624| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.58 r_work: 0.3100 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2968 Z= 0.128 Angle : 0.582 6.048 4033 Z= 0.285 Chirality : 0.039 0.129 514 Planarity : 0.004 0.033 488 Dihedral : 4.014 19.562 405 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.50 % Allowed : 23.57 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.44), residues: 387 helix: 2.22 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.33 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 386 TYR 0.008 0.002 TYR A 4 PHE 0.010 0.001 PHE A 164 TRP 0.002 0.001 TRP A 192 HIS 0.001 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 2968) covalent geometry : angle 0.58187 ( 4033) hydrogen bonds : bond 0.03345 ( 235) hydrogen bonds : angle 4.55780 ( 699) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.116 Fit side-chains REVERT: A 26 GLU cc_start: 0.7781 (tp30) cc_final: 0.7388 (tp30) REVERT: A 61 VAL cc_start: 0.8625 (m) cc_final: 0.8325 (t) REVERT: A 111 ASN cc_start: 0.7899 (p0) cc_final: 0.7661 (OUTLIER) REVERT: A 131 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8340 (mmt) REVERT: A 153 MET cc_start: 0.6367 (mtt) cc_final: 0.6019 (mtp) REVERT: A 255 SER cc_start: 0.8840 (p) cc_final: 0.8492 (p) REVERT: A 312 THR cc_start: 0.8181 (p) cc_final: 0.7965 (p) REVERT: A 325 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8130 (mm) outliers start: 11 outliers final: 6 residues processed: 76 average time/residue: 0.4997 time to fit residues: 39.0965 Evaluate side-chains 73 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 66 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.3980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 27 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.3980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.086044 restraints weight = 4698.312| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.60 r_work: 0.3064 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2968 Z= 0.156 Angle : 0.614 6.869 4033 Z= 0.300 Chirality : 0.040 0.126 514 Planarity : 0.004 0.033 488 Dihedral : 4.083 19.045 405 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.50 % Allowed : 24.52 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.78 (0.44), residues: 387 helix: 2.11 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.24 (1.03), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 229 TYR 0.008 0.002 TYR A 307 PHE 0.014 0.002 PHE A 164 TRP 0.001 0.001 TRP A 192 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 2968) covalent geometry : angle 0.61440 ( 4033) hydrogen bonds : bond 0.03494 ( 235) hydrogen bonds : angle 4.56188 ( 699) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.135 Fit side-chains REVERT: A 26 GLU cc_start: 0.7826 (tp30) cc_final: 0.7413 (tp30) REVERT: A 61 VAL cc_start: 0.8622 (m) cc_final: 0.8295 (t) REVERT: A 111 ASN cc_start: 0.7930 (p0) cc_final: 0.7699 (OUTLIER) REVERT: A 131 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8333 (mmt) REVERT: A 153 MET cc_start: 0.6306 (mtt) cc_final: 0.5948 (mtp) REVERT: A 255 SER cc_start: 0.8888 (p) cc_final: 0.8542 (p) REVERT: A 264 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7739 (mtt) REVERT: A 312 THR cc_start: 0.8216 (p) cc_final: 0.7997 (p) REVERT: A 325 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8110 (mm) outliers start: 11 outliers final: 6 residues processed: 73 average time/residue: 0.5185 time to fit residues: 38.9242 Evaluate side-chains 75 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 67 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.3980 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 5 optimal weight: 0.5980 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.098225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.087181 restraints weight = 4744.492| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 1.61 r_work: 0.3074 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2968 Z= 0.175 Angle : 0.631 7.291 4033 Z= 0.309 Chirality : 0.041 0.131 514 Planarity : 0.004 0.032 488 Dihedral : 4.164 19.000 405 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.87 % Allowed : 24.84 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.69 (0.44), residues: 387 helix: 2.06 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.16 (1.02), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 369 TYR 0.009 0.002 TYR A 307 PHE 0.032 0.002 PHE A 27 TRP 0.001 0.001 TRP A 192 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00431 ( 2968) covalent geometry : angle 0.63122 ( 4033) hydrogen bonds : bond 0.03633 ( 235) hydrogen bonds : angle 4.64289 ( 699) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.119 Fit side-chains REVERT: A 26 GLU cc_start: 0.7827 (tp30) cc_final: 0.7423 (tp30) REVERT: A 61 VAL cc_start: 0.8652 (m) cc_final: 0.8304 (t) REVERT: A 111 ASN cc_start: 0.7928 (p0) cc_final: 0.7687 (OUTLIER) REVERT: A 131 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8369 (mmt) REVERT: A 153 MET cc_start: 0.6404 (mtt) cc_final: 0.6007 (mtp) REVERT: A 211 THR cc_start: 0.8926 (t) cc_final: 0.8609 (p) REVERT: A 255 SER cc_start: 0.8836 (p) cc_final: 0.8492 (p) REVERT: A 312 THR cc_start: 0.8215 (p) cc_final: 0.7993 (p) REVERT: A 313 LEU cc_start: 0.8744 (tm) cc_final: 0.8378 (tt) REVERT: A 325 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8152 (mm) outliers start: 9 outliers final: 6 residues processed: 72 average time/residue: 0.5325 time to fit residues: 39.3941 Evaluate side-chains 74 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 67 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 0.0770 chunk 27 optimal weight: 0.3980 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.4980 chunk 23 optimal weight: 0.4980 chunk 2 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.097093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.085822 restraints weight = 4756.701| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.63 r_work: 0.3055 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2968 Z= 0.162 Angle : 0.634 7.665 4033 Z= 0.310 Chirality : 0.040 0.128 514 Planarity : 0.004 0.033 488 Dihedral : 4.154 19.074 405 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.23 % Allowed : 26.11 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.73 (0.44), residues: 387 helix: 2.07 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.31 (1.03), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 369 TYR 0.008 0.002 TYR A 307 PHE 0.014 0.002 PHE A 11 TRP 0.001 0.001 TRP A 192 HIS 0.002 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 2968) covalent geometry : angle 0.63407 ( 4033) hydrogen bonds : bond 0.03543 ( 235) hydrogen bonds : angle 4.61744 ( 699) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 774 Ramachandran restraints generated. 387 Oldfield, 0 Emsley, 387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.113 Fit side-chains REVERT: A 26 GLU cc_start: 0.7820 (tp30) cc_final: 0.7396 (tp30) REVERT: A 61 VAL cc_start: 0.8619 (m) cc_final: 0.8291 (t) REVERT: A 111 ASN cc_start: 0.7899 (p0) cc_final: 0.7639 (OUTLIER) REVERT: A 131 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8320 (mmt) REVERT: A 153 MET cc_start: 0.6331 (mtt) cc_final: 0.5959 (mtp) REVERT: A 255 SER cc_start: 0.8872 (p) cc_final: 0.8519 (p) REVERT: A 264 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7724 (mtt) REVERT: A 312 THR cc_start: 0.8217 (p) cc_final: 0.7998 (p) REVERT: A 313 LEU cc_start: 0.8734 (tm) cc_final: 0.8374 (tt) REVERT: A 325 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8140 (mm) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.5241 time to fit residues: 38.8089 Evaluate side-chains 73 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 2 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.097746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.086752 restraints weight = 4691.600| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.60 r_work: 0.3066 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2968 Z= 0.199 Angle : 0.664 7.708 4033 Z= 0.325 Chirality : 0.042 0.129 514 Planarity : 0.004 0.032 488 Dihedral : 4.266 18.884 405 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.23 % Allowed : 26.11 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.56 (0.43), residues: 387 helix: 1.97 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.15 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 369 TYR 0.011 0.002 TYR A 307 PHE 0.018 0.002 PHE A 11 TRP 0.001 0.001 TRP A 192 HIS 0.003 0.001 HIS A 219 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 2968) covalent geometry : angle 0.66354 ( 4033) hydrogen bonds : bond 0.03739 ( 235) hydrogen bonds : angle 4.69012 ( 699) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1424.93 seconds wall clock time: 25 minutes 4.41 seconds (1504.41 seconds total)