Starting phenix.real_space_refine on Tue Aug 4 12:05:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k92_62185/08_2026/9k92_62185.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k92_62185/08_2026/9k92_62185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k92_62185/08_2026/9k92_62185.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k92_62185/08_2026/9k92_62185.map" model { file = "/net/cci-nas-00/data/ceres_data/9k92_62185/08_2026/9k92_62185.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k92_62185/08_2026/9k92_62185.cif" } resolution = 3.3 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= -0.000 sd= 0.136 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 18 5.16 5 C 1515 2.51 5 N 333 2.21 5 O 355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2222 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2185 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 4 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Time building chain proxies: 1.08, per 1000 atoms: 0.49 Number of scatterers: 2222 At special positions: 0 Unit cell: (70.3625, 59.5375, 70.3625, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 1 15.00 O 355 8.00 N 333 7.00 C 1515 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: 0.19 Conformation dependent library (CDL) restraints added in 87.4 milliseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 522 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 1 sheets defined 79.9% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'A' and resid 173 through 201 removed outlier: 4.129A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 240 Processing helix chain 'A' and resid 240 through 271 removed outlier: 4.315A pdb=" N TYR A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL A 247 " --> pdb=" O TRP A 243 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 266 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU A 267 " --> pdb=" O CYS A 263 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 Processing helix chain 'A' and resid 312 through 332 removed outlier: 4.098A pdb=" N LEU A 316 " --> pdb=" O TRP A 312 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 362 removed outlier: 3.538A pdb=" N THR A 358 " --> pdb=" O PHE A 354 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.699A pdb=" N LEU A 419 " --> pdb=" O VAL A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 458 Processing helix chain 'A' and resid 464 through 482 Proline residue: A 470 - end of helix removed outlier: 3.569A pdb=" N THR A 475 " --> pdb=" O CYS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 386 through 387 158 hydrogen bonds defined for protein. 471 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: 0.19 Time building geometry restraints manager: 0.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 311 1.29 - 1.42: 600 1.42 - 1.55: 1334 1.55 - 1.68: 2 1.68 - 1.81: 27 Bond restraints: 2274 Sorted by residual: bond pdb=" C21 PC1 A 601 " pdb=" O21 PC1 A 601 " ideal model delta sigma weight residual 1.331 1.433 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 1.330 1.418 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" O13 PC1 A 601 " pdb=" P PC1 A 601 " ideal model delta sigma weight residual 1.652 1.599 0.053 2.00e-02 2.50e+03 7.07e+00 bond pdb=" C33 PC1 A 601 " pdb=" C34 PC1 A 601 " ideal model delta sigma weight residual 1.523 1.479 0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C31 PC1 A 601 " pdb=" O32 PC1 A 601 " ideal model delta sigma weight residual 1.206 1.165 0.041 2.00e-02 2.50e+03 4.17e+00 ... (remaining 2269 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.50: 3062 3.50 - 7.00: 18 7.00 - 10.50: 6 10.50 - 14.00: 2 14.00 - 17.51: 2 Bond angle restraints: 3090 Sorted by residual: angle pdb=" C32 PC1 A 601 " pdb=" C31 PC1 A 601 " pdb=" O31 PC1 A 601 " ideal model delta sigma weight residual 111.44 128.95 -17.51 3.00e+00 1.11e-01 3.41e+01 angle pdb=" C31 PC1 A 601 " pdb=" C32 PC1 A 601 " pdb=" C33 PC1 A 601 " ideal model delta sigma weight residual 113.73 98.66 15.07 3.00e+00 1.11e-01 2.52e+01 angle pdb=" C33 PC1 A 601 " pdb=" C34 PC1 A 601 " pdb=" C35 PC1 A 601 " ideal model delta sigma weight residual 113.40 102.16 11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" C22 PC1 A 601 " pdb=" C21 PC1 A 601 " pdb=" O21 PC1 A 601 " ideal model delta sigma weight residual 111.12 121.74 -10.62 3.00e+00 1.11e-01 1.25e+01 angle pdb=" O31 PC1 A 601 " pdb=" C31 PC1 A 601 " pdb=" O32 PC1 A 601 " ideal model delta sigma weight residual 123.25 114.32 8.93 3.00e+00 1.11e-01 8.86e+00 ... (remaining 3085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.08: 1154 15.08 - 30.16: 121 30.16 - 45.24: 43 45.24 - 60.32: 11 60.32 - 75.40: 1 Dihedral angle restraints: 1330 sinusoidal: 525 harmonic: 805 Sorted by residual: dihedral pdb=" CG ARG A 388 " pdb=" CD ARG A 388 " pdb=" NE ARG A 388 " pdb=" CZ ARG A 388 " ideal model delta sinusoidal sigma weight residual 180.00 -139.37 -40.63 2 1.50e+01 4.44e-03 9.05e+00 dihedral pdb=" CA ILE A 420 " pdb=" CB ILE A 420 " pdb=" CG1 ILE A 420 " pdb=" CD1 ILE A 420 " ideal model delta sinusoidal sigma weight residual 180.00 132.49 47.51 3 1.50e+01 4.44e-03 8.50e+00 dihedral pdb=" CB MET A 486 " pdb=" CG MET A 486 " pdb=" SD MET A 486 " pdb=" CE MET A 486 " ideal model delta sinusoidal sigma weight residual 60.00 106.37 -46.37 3 1.50e+01 4.44e-03 8.32e+00 ... (remaining 1327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 225 0.027 - 0.054: 100 0.054 - 0.081: 36 0.081 - 0.108: 12 0.108 - 0.135: 4 Chirality restraints: 377 Sorted by residual: chirality pdb=" CA THR A 358 " pdb=" N THR A 358 " pdb=" C THR A 358 " pdb=" CB THR A 358 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" C2 PC1 A 601 " pdb=" C1 PC1 A 601 " pdb=" C3 PC1 A 601 " pdb=" O21 PC1 A 601 " both_signs ideal model delta sigma weight residual False -2.49 -2.62 0.13 2.00e-01 2.50e+01 4.18e-01 chirality pdb=" CA ILE A 271 " pdb=" N ILE A 271 " pdb=" C ILE A 271 " pdb=" CB ILE A 271 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 374 not shown) Planarity restraints: 353 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 403 " -0.017 5.00e-02 4.00e+02 2.60e-02 1.08e+00 pdb=" N PRO A 404 " 0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 404 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 404 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C21 PC1 A 601 " 0.016 2.00e-02 2.50e+03 9.03e-03 8.16e-01 pdb=" C22 PC1 A 601 " -0.005 2.00e-02 2.50e+03 pdb=" O21 PC1 A 601 " -0.005 2.00e-02 2.50e+03 pdb=" O22 PC1 A 601 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 415 " 0.015 5.00e-02 4.00e+02 2.24e-02 8.06e-01 pdb=" N PRO A 416 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 416 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 416 " 0.013 5.00e-02 4.00e+02 ... (remaining 350 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 510 2.79 - 3.31: 2177 3.31 - 3.84: 3548 3.84 - 4.37: 3773 4.37 - 4.90: 7037 Nonbonded interactions: 17045 Sorted by model distance: nonbonded pdb=" O ILE A 435 " pdb=" OG SER A 439 " model vdw 2.257 3.040 nonbonded pdb=" O ALA A 184 " pdb=" OH TYR A 437 " model vdw 2.262 3.040 nonbonded pdb=" O21 PC1 A 601 " pdb=" O31 PC1 A 601 " model vdw 2.333 2.432 nonbonded pdb=" C33 PC1 A 601 " pdb=" O32 PC1 A 601 " model vdw 2.364 2.752 nonbonded pdb=" N ASP A 412 " pdb=" OD1 ASP A 412 " model vdw 2.535 3.120 ... (remaining 17040 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: 0.650 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.000 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:0.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 : 0.005 0.102 2274 Z= 0.243 Angle : 0.853 17.506 3090 Z= 0.370 Chirality : 0.037 0.135 377 Planarity : 0.003 0.026 353 Dihedral : 14.910 75.397 808 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % 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: 0.76 (0.53), residues: 264 helix: 1.47 (0.38), residues: 199 sheet: -2.67 (1.22), residues: 10 loop : -2.48 (0.80), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.005 0.001 TYR A 422 PHE 0.007 0.001 PHE A 324 TRP 0.010 0.001 TRP A 303 HIS 0.004 0.003 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.24 ( 2274) covalent geometry : angle 0.85300 / 0.37 ( 3090) hydrogen bonds : bond 0.13477 / 7.56 ( 158) hydrogen bonds : angle 6.26904 / 4.24 ( 471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.089 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0482 time to fit residues: 2.0624 Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.6980 chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 54.3347 > 50:) chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 0.0010 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.0010 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.203687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.154177 restraints weight = 2177.659| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.08 r_work: 0.3360 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.0795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2274 Z= 0.116 Angle : 0.475 7.077 3090 Z= 0.241 Chirality : 0.037 0.134 377 Planarity : 0.004 0.030 353 Dihedral : 10.906 73.201 322 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.24 % Allowed : 14.05 % 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 are not related in a simple way. whole: 1.45 (0.53), residues: 264 helix: 1.98 (0.36), residues: 203 sheet: -2.57 (1.29), residues: 10 loop : -2.64 (0.83), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 307 TYR 0.007 0.001 TYR A 422 PHE 0.007 0.001 PHE A 324 TRP 0.011 0.001 TRP A 189 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 2274) covalent geometry : angle 0.47497 / 0.24 ( 3090) hydrogen bonds : bond 0.03357 / 2.23 ( 158) hydrogen bonds : angle 4.08394 / 2.86 ( 471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 196 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7654 (mm-30) REVERT: A 344 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6982 (mp) REVERT: A 458 MET cc_start: 0.6317 (mtp) cc_final: 0.6068 (mtp) outliers start: 3 outliers final: 2 residues processed: 36 average time/residue: 0.0488 time to fit residues: 2.1154 Evaluate side-chains 38 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 466 LEU Chi-restraints excluded: chain A residue 485 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.202034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147493 restraints weight = 2242.479| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.27 r_work: 0.3372 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2274 Z= 0.123 Angle : 0.462 7.073 3090 Z= 0.232 Chirality : 0.036 0.129 377 Planarity : 0.003 0.027 353 Dihedral : 9.953 69.402 322 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.07 % Allowed : 12.81 % Favored : 85.12 % 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: 1.90 (0.53), residues: 264 helix: 2.27 (0.36), residues: 204 sheet: -2.17 (1.37), residues: 10 loop : -2.44 (0.86), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 307 TYR 0.005 0.001 TYR A 422 PHE 0.009 0.001 PHE A 324 TRP 0.009 0.001 TRP A 189 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 2274) covalent geometry : angle 0.46180 / 0.23 ( 3090) hydrogen bonds : bond 0.02999 / 2.05 ( 158) hydrogen bonds : angle 3.75274 / 2.64 ( 471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: A 183 VAL cc_start: 0.8717 (OUTLIER) cc_final: 0.8437 (t) REVERT: A 344 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7038 (mp) REVERT: A 420 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 458 MET cc_start: 0.6352 (mtp) cc_final: 0.6114 (mtp) REVERT: A 487 LYS cc_start: 0.6653 (mptt) cc_final: 0.6251 (tptt) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 0.0595 time to fit residues: 2.5537 Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 8 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN A 380 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.204172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.148436 restraints weight = 2228.759| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.32 r_work: 0.3401 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2274 Z= 0.143 Angle : 0.483 6.965 3090 Z= 0.242 Chirality : 0.037 0.128 377 Planarity : 0.003 0.029 353 Dihedral : 10.074 69.880 322 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.48 % Allowed : 14.46 % Favored : 83.06 % 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: 2.07 (0.53), residues: 264 helix: 2.42 (0.36), residues: 203 sheet: -2.13 (1.41), residues: 10 loop : -2.44 (0.84), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.005 0.001 TYR A 437 PHE 0.010 0.001 PHE A 324 TRP 0.008 0.001 TRP A 303 HIS 0.001 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 ( 2274) covalent geometry : angle 0.48331 / 0.24 ( 3090) hydrogen bonds : bond 0.03095 / 2.13 ( 158) hydrogen bonds : angle 3.73883 / 2.63 ( 471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.051 Fit side-chains revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7944 (tt) REVERT: A 183 VAL cc_start: 0.8711 (OUTLIER) cc_final: 0.8463 (t) REVERT: A 344 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7088 (mp) REVERT: A 458 MET cc_start: 0.6355 (mtp) cc_final: 0.6071 (mtp) REVERT: A 487 LYS cc_start: 0.6660 (mptt) cc_final: 0.6207 (tptt) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 0.0448 time to fit residues: 1.9116 Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 2 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.203528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.147963 restraints weight = 2205.726| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.30 r_work: 0.3272 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2274 Z= 0.144 Angle : 0.486 6.965 3090 Z= 0.243 Chirality : 0.037 0.128 377 Planarity : 0.003 0.028 353 Dihedral : 9.910 69.438 322 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.89 % Allowed : 14.88 % Favored : 82.23 % 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: 2.11 (0.53), residues: 264 helix: 2.41 (0.36), residues: 203 sheet: -2.07 (1.45), residues: 10 loop : -2.26 (0.85), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 425 TYR 0.005 0.001 TYR A 422 PHE 0.009 0.001 PHE A 324 TRP 0.008 0.001 TRP A 303 HIS 0.001 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 ( 2274) covalent geometry : angle 0.48584 / 0.24 ( 3090) hydrogen bonds : bond 0.03097 / 2.14 ( 158) hydrogen bonds : angle 3.73118 / 2.63 ( 471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8123 (OUTLIER) cc_final: 0.7902 (tt) REVERT: A 183 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8448 (t) REVERT: A 344 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7063 (mp) REVERT: A 420 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.8064 (mt) REVERT: A 458 MET cc_start: 0.6354 (mtp) cc_final: 0.6073 (mtp) REVERT: A 487 LYS cc_start: 0.6590 (mptt) cc_final: 0.6164 (tptt) outliers start: 7 outliers final: 2 residues processed: 39 average time/residue: 0.0685 time to fit residues: 3.1575 Evaluate side-chains 39 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.202355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146776 restraints weight = 2207.976| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.31 r_work: 0.3377 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2274 Z= 0.149 Angle : 0.490 6.872 3090 Z= 0.246 Chirality : 0.037 0.129 377 Planarity : 0.004 0.027 353 Dihedral : 9.982 68.913 322 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.72 % Allowed : 13.22 % Favored : 83.06 % 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: 2.14 (0.53), residues: 264 helix: 2.41 (0.36), residues: 203 sheet: -2.05 (1.48), residues: 10 loop : -2.16 (0.89), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 388 TYR 0.005 0.001 TYR A 422 PHE 0.009 0.001 PHE A 354 TRP 0.008 0.001 TRP A 303 HIS 0.001 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 2274) covalent geometry : angle 0.49002 / 0.25 ( 3090) hydrogen bonds : bond 0.03154 / 2.18 ( 158) hydrogen bonds : angle 3.73392 / 2.63 ( 471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 175 ILE cc_start: 0.8210 (OUTLIER) cc_final: 0.7980 (tt) REVERT: A 183 VAL cc_start: 0.8736 (OUTLIER) cc_final: 0.8456 (t) REVERT: A 344 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7123 (mp) REVERT: A 420 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8110 (mt) REVERT: A 458 MET cc_start: 0.6326 (mtp) cc_final: 0.6043 (mtp) REVERT: A 487 LYS cc_start: 0.6609 (mptt) cc_final: 0.6172 (tptt) outliers start: 9 outliers final: 2 residues processed: 40 average time/residue: 0.0593 time to fit residues: 2.8666 Evaluate side-chains 38 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 3 optimal weight: 0.0470 chunk 21 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.0770 chunk 12 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.205007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150280 restraints weight = 2230.024| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.30 r_work: 0.3435 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2274 Z= 0.102 Angle : 0.457 7.024 3090 Z= 0.229 Chirality : 0.036 0.131 377 Planarity : 0.003 0.024 353 Dihedral : 9.448 69.516 322 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.07 % Allowed : 15.29 % Favored : 82.64 % 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: 2.38 (0.53), residues: 264 helix: 2.51 (0.36), residues: 205 sheet: -1.84 (1.51), residues: 10 loop : -1.92 (0.90), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.008 0.001 TYR A 422 PHE 0.008 0.001 PHE A 354 TRP 0.007 0.001 TRP A 303 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 ( 2274) covalent geometry : angle 0.45744 / 0.23 ( 3090) hydrogen bonds : bond 0.02927 / 2.03 ( 158) hydrogen bonds : angle 3.57055 / 2.53 ( 471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: A 183 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8403 (t) REVERT: A 234 MET cc_start: 0.6980 (mpp) cc_final: 0.6756 (mpp) REVERT: A 344 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7057 (mp) REVERT: A 420 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7983 (mt) REVERT: A 458 MET cc_start: 0.6326 (mtp) cc_final: 0.6064 (mtp) REVERT: A 487 LYS cc_start: 0.6560 (mptt) cc_final: 0.6172 (tptt) outliers start: 5 outliers final: 1 residues processed: 39 average time/residue: 0.0539 time to fit residues: 2.6008 Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.203633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.148201 restraints weight = 2245.655| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.34 r_work: 0.3402 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2274 Z= 0.131 Angle : 0.480 6.725 3090 Z= 0.241 Chirality : 0.037 0.129 377 Planarity : 0.003 0.025 353 Dihedral : 9.583 68.807 322 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.48 % Allowed : 15.29 % Favored : 82.23 % 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: 2.36 (0.53), residues: 264 helix: 2.57 (0.35), residues: 203 sheet: -1.83 (1.48), residues: 10 loop : -2.10 (0.89), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.006 0.001 TYR A 422 PHE 0.008 0.001 PHE A 354 TRP 0.008 0.001 TRP A 303 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 2274) covalent geometry : angle 0.48012 / 0.24 ( 3090) hydrogen bonds : bond 0.03032 / 2.11 ( 158) hydrogen bonds : angle 3.62257 / 2.56 ( 471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 183 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8418 (t) REVERT: A 297 ILE cc_start: 0.6983 (tp) cc_final: 0.6748 (tp) REVERT: A 344 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7120 (mp) REVERT: A 420 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8088 (mt) REVERT: A 458 MET cc_start: 0.6282 (mtp) cc_final: 0.6017 (mtp) REVERT: A 487 LYS cc_start: 0.6571 (mptt) cc_final: 0.6163 (tptt) outliers start: 6 outliers final: 2 residues processed: 38 average time/residue: 0.0673 time to fit residues: 3.0352 Evaluate side-chains 38 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.0060 chunk 18 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.203512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.148388 restraints weight = 2268.263| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.33 r_work: 0.3410 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2274 Z= 0.122 Angle : 0.484 7.659 3090 Z= 0.243 Chirality : 0.037 0.130 377 Planarity : 0.003 0.025 353 Dihedral : 9.539 68.746 322 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.07 % Allowed : 15.29 % Favored : 82.64 % 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: 2.43 (0.53), residues: 264 helix: 2.60 (0.35), residues: 202 sheet: -1.73 (1.50), residues: 10 loop : -1.90 (0.89), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.007 0.001 TYR A 422 PHE 0.008 0.001 PHE A 354 TRP 0.008 0.001 TRP A 303 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 ( 2274) covalent geometry : angle 0.48369 / 0.24 ( 3090) hydrogen bonds : bond 0.02999 / 2.09 ( 158) hydrogen bonds : angle 3.61612 / 2.56 ( 471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.077 Fit side-chains revert: symmetry clash REVERT: A 183 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8264 (t) REVERT: A 297 ILE cc_start: 0.6982 (tp) cc_final: 0.6747 (tp) REVERT: A 344 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7111 (mp) REVERT: A 420 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.8026 (mt) REVERT: A 487 LYS cc_start: 0.6561 (mptt) cc_final: 0.6159 (tptt) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 0.0588 time to fit residues: 2.5669 Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 chunk 18 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.3878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.205841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.150686 restraints weight = 2274.938| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.34 r_work: 0.3443 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2274 Z= 0.102 Angle : 0.476 9.054 3090 Z= 0.237 Chirality : 0.037 0.130 377 Planarity : 0.003 0.024 353 Dihedral : 9.165 68.938 322 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.07 % Allowed : 15.29 % Favored : 82.64 % 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: 2.43 (0.53), residues: 264 helix: 2.54 (0.36), residues: 205 sheet: -1.64 (1.55), residues: 10 loop : -1.92 (0.90), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.008 0.001 TYR A 422 PHE 0.007 0.001 PHE A 354 TRP 0.008 0.001 TRP A 303 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 ( 2274) covalent geometry : angle 0.47560 / 0.24 ( 3090) hydrogen bonds : bond 0.02897 / 2.02 ( 158) hydrogen bonds : angle 3.56049 / 2.53 ( 471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 183 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8238 (t) REVERT: A 420 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.8016 (mt) REVERT: A 487 LYS cc_start: 0.6540 (mptt) cc_final: 0.6157 (tptt) outliers start: 5 outliers final: 2 residues processed: 35 average time/residue: 0.0450 time to fit residues: 2.0292 Evaluate side-chains 36 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 466 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 25 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.200717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.146137 restraints weight = 2261.211| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.31 r_work: 0.3430 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2274 Z= 0.128 Angle : 0.542 10.899 3090 Z= 0.264 Chirality : 0.037 0.143 377 Planarity : 0.003 0.025 353 Dihedral : 9.277 68.497 322 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.07 % Allowed : 15.29 % Favored : 82.64 % 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: 2.34 (0.53), residues: 264 helix: 2.47 (0.36), residues: 205 sheet: -1.77 (1.50), residues: 10 loop : -1.87 (0.91), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.006 0.001 TYR A 422 PHE 0.008 0.001 PHE A 354 TRP 0.008 0.001 TRP A 303 HIS 0.002 0.001 HIS A 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 2274) covalent geometry : angle 0.54152 / 0.26 ( 3090) hydrogen bonds : bond 0.03056 / 2.14 ( 158) hydrogen bonds : angle 3.59776 / 2.55 ( 471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 720.06 seconds wall clock time: 12 minutes 57.14 seconds (777.14 seconds total)