Starting phenix.real_space_refine on Tue Feb 3 13:22:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ugx_64147/02_2026/9ugx_64147.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ugx_64147/02_2026/9ugx_64147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ugx_64147/02_2026/9ugx_64147.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ugx_64147/02_2026/9ugx_64147.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ugx_64147/02_2026/9ugx_64147.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ugx_64147/02_2026/9ugx_64147.map" } resolution = 3.16 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= 0.053 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 2078 2.51 5 N 505 2.21 5 O 557 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3160 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3160 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 15, 'TRANS': 398} Chain breaks: 1 Time building chain proxies: 0.98, per 1000 atoms: 0.31 Number of scatterers: 3160 At special positions: 0 Unit cell: (72.512, 59.328, 69.216, 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 557 8.00 N 505 7.00 C 2078 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: 0.41 Conformation dependent library (CDL) restraints added in 122.4 milliseconds 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 0 sheets defined 51.4% 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 1 through 16 removed outlier: 3.534A pdb=" N TYR A 9 " --> pdb=" O GLY A 5 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.563A pdb=" N ILE A 52 " --> pdb=" O ASP A 48 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 53' Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.775A pdb=" N SER A 81 " --> pdb=" O ARG A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 93 removed outlier: 3.571A pdb=" N VAL A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 96 No H-bonds generated for 'chain 'A' and resid 94 through 96' Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 118 through 122 Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.601A pdb=" N ILE A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 159 removed outlier: 3.558A pdb=" N LEU A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR A 157 " --> pdb=" O PRO A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 184 removed outlier: 3.812A pdb=" N VAL A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 181 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 221 removed outlier: 3.578A pdb=" N LEU A 220 " --> pdb=" O THR A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 232 through 245 removed outlier: 3.770A pdb=" N PHE A 237 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 279 through 291 removed outlier: 3.557A pdb=" N LYS A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.686A pdb=" N THR A 312 " --> pdb=" O MET A 308 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N VAL A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 322 removed outlier: 3.712A pdb=" N VAL A 322 " --> pdb=" O PHE A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 344 removed outlier: 4.024A pdb=" N ILE A 331 " --> pdb=" O PRO A 327 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 332 " --> pdb=" O LYS A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 357 Processing helix chain 'A' and resid 381 through 391 removed outlier: 4.506A pdb=" N ILE A 387 " --> pdb=" O PRO A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 400 removed outlier: 3.626A pdb=" N ALA A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 397 " --> pdb=" O TRP A 393 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TRP A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 270 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: 0.30 Time building geometry restraints manager: 0.51 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: 949 1.34 - 1.46: 888 1.46 - 1.58: 1377 1.58 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 3247 Sorted by residual: bond pdb=" C PRO A 119 " pdb=" N PRO A 120 " ideal model delta sigma weight residual 1.335 1.360 -0.025 9.40e-03 1.13e+04 7.25e+00 bond pdb=" C MET A 35 " pdb=" N PRO A 36 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.27e+00 bond pdb=" C VAL A 100 " pdb=" N PRO A 101 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.30e-02 5.92e+03 3.18e+00 bond pdb=" C LEU A 382 " pdb=" N PRO A 383 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.11e-02 8.12e+03 3.12e+00 bond pdb=" C GLY A 152 " pdb=" N PRO A 153 " ideal model delta sigma weight residual 1.335 1.349 -0.015 1.28e-02 6.10e+03 1.30e+00 ... (remaining 3242 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 4154 2.00 - 3.99: 216 3.99 - 5.99: 32 5.99 - 7.99: 12 7.99 - 9.98: 3 Bond angle restraints: 4417 Sorted by residual: angle pdb=" N SER A 22 " pdb=" CA SER A 22 " pdb=" C SER A 22 " ideal model delta sigma weight residual 114.75 107.35 7.40 1.26e+00 6.30e-01 3.45e+01 angle pdb=" N VAL A 369 " pdb=" CA VAL A 369 " pdb=" C VAL A 369 " ideal model delta sigma weight residual 113.43 107.32 6.11 1.09e+00 8.42e-01 3.14e+01 angle pdb=" N ILE A 368 " pdb=" CA ILE A 368 " pdb=" C ILE A 368 " ideal model delta sigma weight residual 113.43 107.41 6.02 1.09e+00 8.42e-01 3.05e+01 angle pdb=" N VAL A 375 " pdb=" CA VAL A 375 " pdb=" C VAL A 375 " ideal model delta sigma weight residual 113.22 106.53 6.69 1.23e+00 6.61e-01 2.96e+01 angle pdb=" N VAL A 351 " pdb=" CA VAL A 351 " pdb=" C VAL A 351 " ideal model delta sigma weight residual 111.90 107.94 3.96 8.10e-01 1.52e+00 2.39e+01 ... (remaining 4412 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 1536 15.84 - 31.67: 210 31.67 - 47.51: 77 47.51 - 63.34: 17 63.34 - 79.18: 5 Dihedral angle restraints: 1845 sinusoidal: 671 harmonic: 1174 Sorted by residual: dihedral pdb=" CA SER A 81 " pdb=" C SER A 81 " pdb=" N SER A 82 " pdb=" CA SER A 82 " ideal model delta harmonic sigma weight residual 180.00 159.68 20.32 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA ASN A 91 " pdb=" CB ASN A 91 " pdb=" CG ASN A 91 " pdb=" OD1 ASN A 91 " ideal model delta sinusoidal sigma weight residual 120.00 -165.67 -74.33 2 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA PHE A 18 " pdb=" C PHE A 18 " pdb=" N GLY A 19 " pdb=" CA GLY A 19 " ideal model delta harmonic sigma weight residual 180.00 163.80 16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 374 0.045 - 0.090: 102 0.090 - 0.135: 20 0.135 - 0.181: 2 0.181 - 0.226: 1 Chirality restraints: 499 Sorted by residual: chirality pdb=" CB ILE A 187 " pdb=" CA ILE A 187 " pdb=" CG1 ILE A 187 " pdb=" CG2 ILE A 187 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB THR A 99 " pdb=" CA THR A 99 " pdb=" OG1 THR A 99 " pdb=" CG2 THR A 99 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CB VAL A 194 " pdb=" CA VAL A 194 " pdb=" CG1 VAL A 194 " pdb=" CG2 VAL A 194 " both_signs ideal model delta sigma weight residual False -2.63 -2.78 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 496 not shown) Planarity restraints: 542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 152 " -0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO A 153 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 153 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 153 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 42 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO A 43 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 326 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO A 327 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 327 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 327 " 0.030 5.00e-02 4.00e+02 ... (remaining 539 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 342 2.74 - 3.28: 3009 3.28 - 3.82: 5207 3.82 - 4.36: 6670 4.36 - 4.90: 11061 Nonbonded interactions: 26289 Sorted by model distance: nonbonded pdb=" O LEU A 317 " pdb=" OG1 THR A 321 " model vdw 2.199 3.040 nonbonded pdb=" O PHE A 412 " pdb=" NH1 ARG A 415 " model vdw 2.298 3.120 nonbonded pdb=" O GLU A 219 " pdb=" OG SER A 223 " model vdw 2.305 3.040 nonbonded pdb=" NH1 ARG A 319 " pdb=" OE1 GLU A 401 " model vdw 2.333 3.120 nonbonded pdb=" O LEU A 23 " pdb=" ND2 ASN A 27 " model vdw 2.337 3.120 ... (remaining 26284 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: 0.560 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.030 Process input model: 5.380 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:0.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 0.025 3247 Z= 0.185 Angle : 1.047 9.983 4417 Z= 0.696 Chirality : 0.043 0.226 499 Planarity : 0.006 0.058 542 Dihedral : 17.712 79.175 1099 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.00 % Allowed : 29.43 % Favored : 70.57 % 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 are not related in a simple way. whole: -5.64 (0.34), residues: 410 helix: -3.80 (0.21), residues: 331 sheet: None (None), residues: 0 loop : -1.88 (0.74), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 423 TYR 0.011 0.001 TYR A 6 PHE 0.008 0.001 PHE A 340 TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 3247) covalent geometry : angle 1.04736 ( 4417) hydrogen bonds : bond 0.23917 ( 94) hydrogen bonds : angle 10.58337 ( 270) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.110 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.0882 time to fit residues: 4.7207 Evaluate side-chains 41 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.0370 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.0040 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.3268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 295 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128929 restraints weight = 3980.193| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.95 r_work: 0.3432 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3247 Z= 0.106 Angle : 0.646 8.441 4417 Z= 0.338 Chirality : 0.040 0.183 499 Planarity : 0.006 0.052 542 Dihedral : 5.956 19.294 440 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.60 % Allowed : 27.33 % Favored : 69.07 % 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 are not related in a simple way. whole: -5.08 (0.35), residues: 410 helix: -3.38 (0.22), residues: 334 sheet: None (None), residues: 0 loop : -1.73 (0.76), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.012 0.001 TYR A 233 PHE 0.008 0.001 PHE A 134 TRP 0.006 0.001 TRP A 107 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 3247) covalent geometry : angle 0.64568 ( 4417) hydrogen bonds : bond 0.03222 ( 94) hydrogen bonds : angle 5.23778 ( 270) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.121 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 60 average time/residue: 0.0730 time to fit residues: 5.3260 Evaluate side-chains 50 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 407 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 20 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.149569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.122571 restraints weight = 3975.114| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.99 r_work: 0.3327 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3247 Z= 0.142 Angle : 0.627 7.113 4417 Z= 0.328 Chirality : 0.041 0.199 499 Planarity : 0.005 0.052 542 Dihedral : 5.695 18.588 440 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.50 % Allowed : 25.53 % Favored : 69.97 % 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 are not related in a simple way. whole: -4.69 (0.37), residues: 410 helix: -3.12 (0.23), residues: 334 sheet: None (None), residues: 0 loop : -1.56 (0.78), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.009 0.001 TYR A 25 PHE 0.007 0.001 PHE A 340 TRP 0.007 0.001 TRP A 107 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 3247) covalent geometry : angle 0.62711 ( 4417) hydrogen bonds : bond 0.02873 ( 94) hydrogen bonds : angle 4.63283 ( 270) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.076 Fit side-chains REVERT: A 269 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 418 ARG cc_start: 0.8116 (ptm160) cc_final: 0.7847 (ptm160) outliers start: 15 outliers final: 9 residues processed: 55 average time/residue: 0.0607 time to fit residues: 3.9969 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 375 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 4 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.145130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117570 restraints weight = 3920.510| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.97 r_work: 0.3262 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3247 Z= 0.167 Angle : 0.612 6.374 4417 Z= 0.321 Chirality : 0.042 0.148 499 Planarity : 0.005 0.050 542 Dihedral : 5.600 18.963 440 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 6.61 % Allowed : 24.32 % Favored : 69.07 % 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 are not related in a simple way. whole: -4.29 (0.38), residues: 410 helix: -2.83 (0.24), residues: 334 sheet: None (None), residues: 0 loop : -1.45 (0.79), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.011 0.001 TYR A 25 PHE 0.008 0.001 PHE A 340 TRP 0.007 0.001 TRP A 107 HIS 0.002 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 3247) covalent geometry : angle 0.61242 ( 4417) hydrogen bonds : bond 0.02683 ( 94) hydrogen bonds : angle 4.39058 ( 270) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 39 time to evaluate : 0.068 Fit side-chains REVERT: A 269 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8250 (tt) outliers start: 22 outliers final: 11 residues processed: 57 average time/residue: 0.0420 time to fit residues: 3.0595 Evaluate side-chains 48 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 408 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.147031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.119551 restraints weight = 3931.871| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.98 r_work: 0.3168 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3247 Z= 0.127 Angle : 0.573 6.018 4417 Z= 0.300 Chirality : 0.040 0.140 499 Planarity : 0.005 0.046 542 Dihedral : 5.418 18.831 440 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 5.41 % Allowed : 25.53 % Favored : 69.07 % 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 are not related in a simple way. whole: -3.98 (0.38), residues: 410 helix: -2.62 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -1.40 (0.78), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 300 TYR 0.008 0.001 TYR A 24 PHE 0.007 0.001 PHE A 340 TRP 0.007 0.001 TRP A 107 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 3247) covalent geometry : angle 0.57343 ( 4417) hydrogen bonds : bond 0.02504 ( 94) hydrogen bonds : angle 4.23344 ( 270) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 46 time to evaluate : 0.116 Fit side-chains REVERT: A 269 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8411 (tt) outliers start: 18 outliers final: 12 residues processed: 60 average time/residue: 0.0613 time to fit residues: 4.6207 Evaluate side-chains 55 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 361 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 0.0070 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.148582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.120956 restraints weight = 3899.831| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.97 r_work: 0.3302 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3247 Z= 0.111 Angle : 0.563 6.563 4417 Z= 0.290 Chirality : 0.039 0.136 499 Planarity : 0.004 0.045 542 Dihedral : 5.235 19.277 440 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.90 % Allowed : 28.23 % Favored : 67.87 % 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 are not related in a simple way. whole: -3.53 (0.39), residues: 410 helix: -2.31 (0.26), residues: 333 sheet: None (None), residues: 0 loop : -1.20 (0.78), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.007 0.001 TYR A 24 PHE 0.007 0.001 PHE A 340 TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 3247) covalent geometry : angle 0.56286 ( 4417) hydrogen bonds : bond 0.02322 ( 94) hydrogen bonds : angle 4.04117 ( 270) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.109 Fit side-chains REVERT: A 10 ARG cc_start: 0.7735 (ttm170) cc_final: 0.7528 (ttm170) REVERT: A 269 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8290 (tt) outliers start: 13 outliers final: 11 residues processed: 48 average time/residue: 0.0708 time to fit residues: 4.1952 Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 243 CYS Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 361 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.147279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.119260 restraints weight = 3974.755| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 2.04 r_work: 0.3281 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3247 Z= 0.117 Angle : 0.549 5.966 4417 Z= 0.283 Chirality : 0.040 0.149 499 Planarity : 0.004 0.045 542 Dihedral : 5.116 19.562 440 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 4.80 % Allowed : 27.63 % Favored : 67.57 % 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 are not related in a simple way. whole: -3.10 (0.40), residues: 410 helix: -2.01 (0.27), residues: 333 sheet: None (None), residues: 0 loop : -1.05 (0.79), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.007 0.001 TYR A 24 PHE 0.007 0.001 PHE A 340 TRP 0.007 0.001 TRP A 107 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 3247) covalent geometry : angle 0.54913 ( 4417) hydrogen bonds : bond 0.02216 ( 94) hydrogen bonds : angle 3.94502 ( 270) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.122 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 52 average time/residue: 0.0671 time to fit residues: 4.3502 Evaluate side-chains 53 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 258 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 361 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 21 optimal weight: 0.0970 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3717 r_free = 0.3717 target = 0.149405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.121712 restraints weight = 3973.010| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.02 r_work: 0.3314 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3247 Z= 0.097 Angle : 0.549 7.672 4417 Z= 0.278 Chirality : 0.040 0.204 499 Planarity : 0.004 0.043 542 Dihedral : 4.988 18.658 440 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 3.90 % Allowed : 28.53 % Favored : 67.57 % 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 are not related in a simple way. whole: -2.71 (0.41), residues: 410 helix: -1.74 (0.27), residues: 334 sheet: None (None), residues: 0 loop : -0.89 (0.80), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.009 0.001 TYR A 6 PHE 0.007 0.001 PHE A 340 TRP 0.007 0.001 TRP A 107 HIS 0.002 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 3247) covalent geometry : angle 0.54866 ( 4417) hydrogen bonds : bond 0.02127 ( 94) hydrogen bonds : angle 3.81228 ( 270) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 0.071 Fit side-chains REVERT: A 171 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7995 (tp) outliers start: 13 outliers final: 10 residues processed: 44 average time/residue: 0.0419 time to fit residues: 2.4518 Evaluate side-chains 44 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 361 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.0030 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 overall best weight: 0.3790 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.151353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.123995 restraints weight = 3910.478| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.99 r_work: 0.3337 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3247 Z= 0.089 Angle : 0.536 6.942 4417 Z= 0.270 Chirality : 0.039 0.200 499 Planarity : 0.004 0.043 542 Dihedral : 4.819 18.279 440 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.20 % Allowed : 28.83 % Favored : 66.97 % 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 are not related in a simple way. whole: -2.23 (0.42), residues: 410 helix: -1.40 (0.28), residues: 337 sheet: None (None), residues: 0 loop : -0.73 (0.85), residues: 73 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.005 0.001 TYR A 24 PHE 0.006 0.001 PHE A 340 TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 3247) covalent geometry : angle 0.53596 ( 4417) hydrogen bonds : bond 0.02047 ( 94) hydrogen bonds : angle 3.70127 ( 270) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 35 time to evaluate : 0.113 Fit side-chains REVERT: A 171 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7916 (tp) outliers start: 14 outliers final: 12 residues processed: 43 average time/residue: 0.0450 time to fit residues: 2.6759 Evaluate side-chains 45 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 37 optimal weight: 0.0870 chunk 27 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 21 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN ** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.152424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125186 restraints weight = 3897.797| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.00 r_work: 0.3340 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3247 Z= 0.087 Angle : 0.545 6.877 4417 Z= 0.271 Chirality : 0.039 0.196 499 Planarity : 0.004 0.042 542 Dihedral : 4.735 18.111 440 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.20 % Allowed : 28.23 % Favored : 67.57 % 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 are not related in a simple way. whole: -1.83 (0.43), residues: 410 helix: -1.13 (0.29), residues: 333 sheet: None (None), residues: 0 loop : -0.61 (0.83), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.005 0.001 TYR A 24 PHE 0.006 0.001 PHE A 340 TRP 0.007 0.001 TRP A 107 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 3247) covalent geometry : angle 0.54549 ( 4417) hydrogen bonds : bond 0.01988 ( 94) hydrogen bonds : angle 3.79955 ( 270) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 820 Ramachandran restraints generated. 410 Oldfield, 0 Emsley, 410 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.120 Fit side-chains REVERT: A 171 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7855 (tp) outliers start: 14 outliers final: 12 residues processed: 39 average time/residue: 0.0470 time to fit residues: 2.5528 Evaluate side-chains 44 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 107 TRP Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 361 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 298 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 = 0.3710 r_free = 0.3710 target = 0.149326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.121415 restraints weight = 3974.777| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.02 r_work: 0.3284 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3247 Z= 0.109 Angle : 0.551 7.057 4417 Z= 0.275 Chirality : 0.040 0.197 499 Planarity : 0.004 0.043 542 Dihedral : 4.775 19.141 440 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.60 % Allowed : 28.83 % Favored : 67.57 % 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 are not related in a simple way. whole: -1.71 (0.43), residues: 410 helix: -1.04 (0.29), residues: 336 sheet: None (None), residues: 0 loop : -0.58 (0.87), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 10 TYR 0.006 0.001 TYR A 233 PHE 0.007 0.001 PHE A 340 TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3247) covalent geometry : angle 0.55104 ( 4417) hydrogen bonds : bond 0.02025 ( 94) hydrogen bonds : angle 3.88260 ( 270) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 973.08 seconds wall clock time: 17 minutes 23.88 seconds (1043.88 seconds total)