Starting phenix.real_space_refine on Tue Feb 3 12:43:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k93_62186/02_2026/9k93_62186.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k93_62186/02_2026/9k93_62186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k93_62186/02_2026/9k93_62186.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k93_62186/02_2026/9k93_62186.map" model { file = "/net/cci-nas-00/data/ceres_data/9k93_62186/02_2026/9k93_62186.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k93_62186/02_2026/9k93_62186.cif" } resolution = 3.6 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= 0.003 sd= 0.131 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 18 5.16 5 C 1580 2.51 5 N 344 2.21 5 O 365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 2307 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2258 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain breaks: 5 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'FTO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.67, per 1000 atoms: 0.29 Number of scatterers: 2307 At special positions: 0 Unit cell: (72.5275, 58.455, 70.3625, 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 18 16.00 O 365 8.00 N 344 7.00 C 1580 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: 0.13 Conformation dependent library (CDL) restraints added in 53.4 milliseconds 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 538 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 82.7% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 169 through 199 removed outlier: 3.791A pdb=" N VAL A 173 " --> pdb=" O ASP A 169 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 240 Processing helix chain 'A' and resid 240 through 270 removed outlier: 4.500A pdb=" N TYR A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 Processing helix chain 'A' and resid 312 through 332 removed outlier: 4.526A pdb=" N LEU A 316 " --> pdb=" O TRP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 357 Processing helix chain 'A' and resid 358 through 361 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 409 through 431 removed outlier: 3.991A pdb=" N ILE A 413 " --> pdb=" O GLY A 409 " (cutoff:3.500A) Proline residue: A 416 - end of helix Processing helix chain 'A' and resid 434 through 459 Processing helix chain 'A' and resid 464 through 483 Proline residue: A 470 - end of helix removed outlier: 4.189A pdb=" N ARG A 483 " --> pdb=" O VAL A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 390 173 hydrogen bonds defined for protein. 513 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: 0.25 Time building geometry restraints manager: 0.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 322 1.31 - 1.43: 663 1.43 - 1.56: 1352 1.56 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 2364 Sorted by residual: bond pdb=" C16 FTO A 601 " pdb=" N17 FTO A 601 " ideal model delta sigma weight residual 1.337 1.449 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C13 FTO A 601 " pdb=" N14 FTO A 601 " ideal model delta sigma weight residual 1.340 1.449 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C10 FTO A 601 " pdb=" N11 FTO A 601 " ideal model delta sigma weight residual 1.347 1.452 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C04 FTO A 601 " pdb=" N05 FTO A 601 " ideal model delta sigma weight residual 1.350 1.453 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C04 FTO A 601 " pdb=" O03 FTO A 601 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 2359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 3156 2.15 - 4.31: 33 4.31 - 6.46: 18 6.46 - 8.62: 5 8.62 - 10.77: 1 Bond angle restraints: 3213 Sorted by residual: angle pdb=" N05 FTO A 601 " pdb=" C04 FTO A 601 " pdb=" O03 FTO A 601 " ideal model delta sigma weight residual 109.59 120.36 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N PHE A 218 " pdb=" CA PHE A 218 " pdb=" C PHE A 218 " ideal model delta sigma weight residual 110.52 114.38 -3.86 1.48e+00 4.57e-01 6.79e+00 angle pdb=" C12 FTO A 601 " pdb=" C27 FTO A 601 " pdb=" C28 FTO A 601 " ideal model delta sigma weight residual 117.33 109.89 7.44 3.00e+00 1.11e-01 6.16e+00 angle pdb=" N ASP A 427 " pdb=" CA ASP A 427 " pdb=" C ASP A 427 " ideal model delta sigma weight residual 111.07 108.56 2.51 1.07e+00 8.73e-01 5.50e+00 angle pdb=" CB MET A 248 " pdb=" CG MET A 248 " pdb=" SD MET A 248 " ideal model delta sigma weight residual 112.70 119.63 -6.93 3.00e+00 1.11e-01 5.33e+00 ... (remaining 3208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.42: 1296 34.42 - 68.84: 49 68.84 - 103.26: 1 103.26 - 137.68: 0 137.68 - 172.10: 1 Dihedral angle restraints: 1347 sinusoidal: 518 harmonic: 829 Sorted by residual: dihedral pdb=" C12 FTO A 601 " pdb=" C27 FTO A 601 " pdb=" C28 FTO A 601 " pdb=" C30 FTO A 601 " ideal model delta sinusoidal sigma weight residual 91.82 -96.08 -172.10 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA TYR A 241 " pdb=" C TYR A 241 " pdb=" N LYS A 242 " pdb=" CA LYS A 242 " ideal model delta harmonic sigma weight residual 180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CG ARG A 482 " pdb=" CD ARG A 482 " pdb=" NE ARG A 482 " pdb=" CZ ARG A 482 " ideal model delta sinusoidal sigma weight residual 180.00 135.01 44.99 2 1.50e+01 4.44e-03 1.07e+01 ... (remaining 1344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 346 0.055 - 0.109: 41 0.109 - 0.163: 4 0.163 - 0.218: 0 0.218 - 0.272: 1 Chirality restraints: 392 Sorted by residual: chirality pdb=" C12 FTO A 601 " pdb=" C13 FTO A 601 " pdb=" C27 FTO A 601 " pdb=" N11 FTO A 601 " both_signs ideal model delta sigma weight residual False 2.42 2.70 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C06 FTO A 601 " pdb=" C07 FTO A 601 " pdb=" C40 FTO A 601 " pdb=" N05 FTO A 601 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.32e-01 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 2.40 0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 389 not shown) Planarity restraints: 367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 217 " -0.006 2.00e-02 2.50e+03 1.22e-02 1.49e+00 pdb=" C THR A 217 " 0.021 2.00e-02 2.50e+03 pdb=" O THR A 217 " -0.008 2.00e-02 2.50e+03 pdb=" N PHE A 218 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 353 " 0.006 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C PHE A 353 " -0.019 2.00e-02 2.50e+03 pdb=" O PHE A 353 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE A 354 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 465 " 0.005 2.00e-02 2.50e+03 9.15e-03 8.36e-01 pdb=" C LEU A 465 " -0.016 2.00e-02 2.50e+03 pdb=" O LEU A 465 " 0.006 2.00e-02 2.50e+03 pdb=" N LEU A 466 " 0.005 2.00e-02 2.50e+03 ... (remaining 364 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 31 2.69 - 3.24: 2329 3.24 - 3.80: 3551 3.80 - 4.35: 4166 4.35 - 4.90: 7366 Nonbonded interactions: 17443 Sorted by model distance: nonbonded pdb=" O PHE A 168 " pdb=" OD1 ASP A 169 " model vdw 2.141 3.040 nonbonded pdb=" O ALA A 184 " pdb=" OH TYR A 437 " model vdw 2.235 3.040 nonbonded pdb=" O PHE A 354 " pdb=" OG1 THR A 358 " model vdw 2.319 3.040 nonbonded pdb=" O LEU A 236 " pdb=" CD1 LEU A 244 " model vdw 2.326 3.460 nonbonded pdb=" OE1 GLU A 309 " pdb=" NE1 TRP A 312 " model vdw 2.371 3.120 ... (remaining 17438 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.640 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 3.990 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 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 : 0.006 0.112 2364 Z= 0.313 Angle : 0.725 10.770 3213 Z= 0.314 Chirality : 0.040 0.272 392 Planarity : 0.003 0.019 367 Dihedral : 17.936 172.096 809 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 28.40 % Favored : 71.60 % 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: 1.86 (0.52), residues: 270 helix: 2.21 (0.36), residues: 201 sheet: -2.51 (1.46), residues: 10 loop : -1.64 (0.75), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.008 0.001 TYR A 444 PHE 0.012 0.001 PHE A 489 TRP 0.005 0.001 TRP A 490 HIS 0.000 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 2364) covalent geometry : angle 0.72490 ( 3213) hydrogen bonds : bond 0.15808 ( 173) hydrogen bonds : angle 5.80544 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.051 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.0420 time to fit residues: 1.9546 Evaluate side-chains 36 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN A 462 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.183560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.160981 restraints weight = 2657.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.165315 restraints weight = 1526.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.168137 restraints weight = 1058.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.170191 restraints weight = 822.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.171665 restraints weight = 679.656| |-----------------------------------------------------------------------------| r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2364 Z= 0.128 Angle : 0.530 7.472 3213 Z= 0.261 Chirality : 0.037 0.134 392 Planarity : 0.003 0.026 367 Dihedral : 11.455 175.960 306 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.40 % Allowed : 26.80 % Favored : 68.80 % 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: 2.42 (0.52), residues: 270 helix: 2.48 (0.36), residues: 202 sheet: -1.98 (1.34), residues: 10 loop : -1.00 (0.87), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.008 0.001 TYR A 436 PHE 0.010 0.001 PHE A 489 TRP 0.007 0.001 TRP A 490 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2364) covalent geometry : angle 0.52994 ( 3213) hydrogen bonds : bond 0.04823 ( 173) hydrogen bonds : angle 3.90122 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.048 Fit side-chains revert: symmetry clash REVERT: A 475 THR cc_start: 0.7747 (OUTLIER) cc_final: 0.7536 (t) outliers start: 11 outliers final: 7 residues processed: 42 average time/residue: 0.0441 time to fit residues: 2.1744 Evaluate side-chains 39 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3812 r_free = 0.3812 target = 0.158060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136749 restraints weight = 2712.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.141027 restraints weight = 1458.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.143940 restraints weight = 966.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.146084 restraints weight = 727.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147538 restraints weight = 583.479| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2364 Z= 0.220 Angle : 0.628 6.865 3213 Z= 0.314 Chirality : 0.040 0.138 392 Planarity : 0.004 0.036 367 Dihedral : 11.489 172.838 306 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 10.00 % Allowed : 23.60 % Favored : 66.40 % 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: 1.87 (0.52), residues: 270 helix: 1.98 (0.35), residues: 205 sheet: -1.87 (1.25), residues: 10 loop : -0.96 (0.92), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.012 0.001 TYR A 422 PHE 0.014 0.001 PHE A 489 TRP 0.008 0.002 TRP A 243 HIS 0.000 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00512 ( 2364) covalent geometry : angle 0.62798 ( 3213) hydrogen bonds : bond 0.05074 ( 173) hydrogen bonds : angle 4.14160 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 36 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: A 475 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7454 (t) outliers start: 25 outliers final: 17 residues processed: 55 average time/residue: 0.0487 time to fit residues: 3.2744 Evaluate side-chains 53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 35 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 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 = 0.3876 r_free = 0.3876 target = 0.164233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.141961 restraints weight = 2668.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.146628 restraints weight = 1384.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149902 restraints weight = 900.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.152186 restraints weight = 663.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.153622 restraints weight = 525.488| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2364 Z= 0.140 Angle : 0.515 5.279 3213 Z= 0.255 Chirality : 0.037 0.127 392 Planarity : 0.003 0.036 367 Dihedral : 11.357 171.392 306 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 10.00 % Allowed : 25.60 % Favored : 64.40 % 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 (0.52), residues: 270 helix: 2.37 (0.35), residues: 203 sheet: -1.55 (1.34), residues: 10 loop : -0.83 (0.92), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.010 0.001 TYR A 422 PHE 0.013 0.001 PHE A 489 TRP 0.007 0.001 TRP A 490 HIS 0.001 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2364) covalent geometry : angle 0.51503 ( 3213) hydrogen bonds : bond 0.04372 ( 173) hydrogen bonds : angle 3.92842 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 34 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: A 354 PHE cc_start: 0.6079 (OUTLIER) cc_final: 0.5583 (m-10) REVERT: A 475 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7415 (t) outliers start: 25 outliers final: 16 residues processed: 54 average time/residue: 0.0351 time to fit residues: 2.2951 Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 34 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.163571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.140993 restraints weight = 2629.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.145640 restraints weight = 1383.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148878 restraints weight = 901.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.151150 restraints weight = 667.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.152746 restraints weight = 534.035| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2364 Z= 0.157 Angle : 0.540 5.299 3213 Z= 0.267 Chirality : 0.038 0.134 392 Planarity : 0.004 0.038 367 Dihedral : 11.290 169.697 306 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 11.60 % Allowed : 24.80 % Favored : 63.60 % 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 (0.52), residues: 270 helix: 2.33 (0.35), residues: 203 sheet: -1.44 (1.38), residues: 10 loop : -0.82 (0.90), residues: 57 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 0.013 0.001 PHE A 489 TRP 0.006 0.001 TRP A 490 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2364) covalent geometry : angle 0.54047 ( 3213) hydrogen bonds : bond 0.04456 ( 173) hydrogen bonds : angle 3.95818 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 30 time to evaluate : 0.081 Fit side-chains revert: symmetry clash REVERT: A 354 PHE cc_start: 0.6234 (OUTLIER) cc_final: 0.5757 (m-10) REVERT: A 475 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7478 (t) outliers start: 29 outliers final: 24 residues processed: 55 average time/residue: 0.0586 time to fit residues: 3.8681 Evaluate side-chains 56 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 30 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 13 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3890 r_free = 0.3890 target = 0.165836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.143396 restraints weight = 2616.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.148165 restraints weight = 1376.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.151447 restraints weight = 891.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.153669 restraints weight = 658.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.155293 restraints weight = 525.307| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2364 Z= 0.121 Angle : 0.494 5.275 3213 Z= 0.243 Chirality : 0.037 0.123 392 Planarity : 0.003 0.037 367 Dihedral : 11.113 167.283 306 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 9.60 % Allowed : 27.60 % Favored : 62.80 % 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: 2.63 (0.52), residues: 270 helix: 2.53 (0.35), residues: 204 sheet: -0.88 (1.48), residues: 10 loop : -0.85 (0.90), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.007 0.001 TYR A 422 PHE 0.012 0.001 PHE A 489 TRP 0.007 0.001 TRP A 490 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2364) covalent geometry : angle 0.49377 ( 3213) hydrogen bonds : bond 0.04068 ( 173) hydrogen bonds : angle 3.84183 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 31 time to evaluate : 0.049 Fit side-chains revert: symmetry clash REVERT: A 354 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5521 (m-10) REVERT: A 475 THR cc_start: 0.7672 (OUTLIER) cc_final: 0.7443 (t) outliers start: 24 outliers final: 17 residues processed: 50 average time/residue: 0.0397 time to fit residues: 2.4074 Evaluate side-chains 50 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 31 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 249 ILE Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.0170 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 0.0170 chunk 27 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.3856 ------------------------------------------------------------------------------- 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 = 0.3877 r_free = 0.3877 target = 0.164547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.141995 restraints weight = 2620.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146648 restraints weight = 1407.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.149805 restraints weight = 926.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.151936 restraints weight = 693.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.153117 restraints weight = 559.288| |-----------------------------------------------------------------------------| r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2364 Z= 0.103 Angle : 0.486 6.302 3213 Z= 0.235 Chirality : 0.036 0.120 392 Planarity : 0.003 0.037 367 Dihedral : 10.840 163.452 306 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 7.20 % Allowed : 29.20 % Favored : 63.60 % 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: 2.87 (0.52), residues: 270 helix: 2.73 (0.36), residues: 204 sheet: -0.55 (1.47), residues: 10 loop : -0.91 (0.89), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 311 TYR 0.005 0.001 TYR A 422 PHE 0.011 0.001 PHE A 489 TRP 0.007 0.001 TRP A 490 HIS 0.001 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 2364) covalent geometry : angle 0.48590 ( 3213) hydrogen bonds : bond 0.03791 ( 173) hydrogen bonds : angle 3.75575 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 31 time to evaluate : 0.084 Fit side-chains revert: symmetry clash REVERT: A 350 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6132 (t80) REVERT: A 354 PHE cc_start: 0.6057 (OUTLIER) cc_final: 0.5434 (m-10) REVERT: A 475 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.7323 (t) outliers start: 18 outliers final: 12 residues processed: 46 average time/residue: 0.0658 time to fit residues: 3.5806 Evaluate side-chains 46 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 18 optimal weight: 0.0470 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3885 r_free = 0.3885 target = 0.164934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143050 restraints weight = 2584.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.147648 restraints weight = 1396.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.150695 restraints weight = 918.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.152336 restraints weight = 689.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.154027 restraints weight = 575.142| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2364 Z= 0.120 Angle : 0.518 6.146 3213 Z= 0.246 Chirality : 0.036 0.124 392 Planarity : 0.003 0.038 367 Dihedral : 10.737 161.942 306 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 8.80 % Allowed : 27.60 % Favored : 63.60 % 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: 2.84 (0.52), residues: 270 helix: 2.70 (0.35), residues: 204 sheet: -0.44 (1.50), residues: 10 loop : -0.89 (0.90), residues: 56 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 0.011 0.001 PHE A 489 TRP 0.006 0.001 TRP A 490 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2364) covalent geometry : angle 0.51760 ( 3213) hydrogen bonds : bond 0.03901 ( 173) hydrogen bonds : angle 3.76872 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 31 time to evaluate : 0.051 Fit side-chains revert: symmetry clash REVERT: A 350 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6311 (t80) REVERT: A 354 PHE cc_start: 0.5960 (OUTLIER) cc_final: 0.5464 (m-10) REVERT: A 475 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7374 (t) outliers start: 22 outliers final: 18 residues processed: 50 average time/residue: 0.0516 time to fit residues: 3.0352 Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 31 time to evaluate : 0.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.0980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.164873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.142856 restraints weight = 2646.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.147358 restraints weight = 1426.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.150503 restraints weight = 943.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.152617 restraints weight = 703.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154320 restraints weight = 568.143| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2364 Z= 0.121 Angle : 0.510 6.529 3213 Z= 0.244 Chirality : 0.037 0.123 392 Planarity : 0.003 0.037 367 Dihedral : 10.658 161.086 306 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 8.00 % Allowed : 28.80 % Favored : 63.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.86 (0.52), residues: 270 helix: 2.70 (0.35), residues: 204 sheet: -0.42 (1.50), residues: 10 loop : -0.87 (0.90), residues: 56 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 0.012 0.001 PHE A 489 TRP 0.006 0.001 TRP A 490 HIS 0.001 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 2364) covalent geometry : angle 0.51005 ( 3213) hydrogen bonds : bond 0.03929 ( 173) hydrogen bonds : angle 3.75103 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.080 Fit side-chains revert: symmetry clash REVERT: A 350 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6439 (t80) REVERT: A 475 THR cc_start: 0.7592 (OUTLIER) cc_final: 0.7360 (t) outliers start: 20 outliers final: 18 residues processed: 48 average time/residue: 0.0624 time to fit residues: 3.5587 Evaluate side-chains 51 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 31 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3880 r_free = 0.3880 target = 0.164509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141858 restraints weight = 2674.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.146601 restraints weight = 1389.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.149866 restraints weight = 901.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152106 restraints weight = 666.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.153687 restraints weight = 531.880| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2364 Z= 0.120 Angle : 0.513 6.922 3213 Z= 0.246 Chirality : 0.037 0.124 392 Planarity : 0.003 0.038 367 Dihedral : 10.579 160.116 306 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 8.80 % Allowed : 28.80 % Favored : 62.40 % 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: 2.84 (0.52), residues: 270 helix: 2.69 (0.35), residues: 204 sheet: -0.42 (1.50), residues: 10 loop : -0.87 (0.91), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 288 TYR 0.006 0.001 TYR A 422 PHE 0.011 0.001 PHE A 489 TRP 0.006 0.001 TRP A 490 HIS 0.001 0.000 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 2364) covalent geometry : angle 0.51340 ( 3213) hydrogen bonds : bond 0.03890 ( 173) hydrogen bonds : angle 3.78795 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 540 Ramachandran restraints generated. 270 Oldfield, 0 Emsley, 270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 31 time to evaluate : 0.047 Fit side-chains revert: symmetry clash REVERT: A 350 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6401 (t80) REVERT: A 475 THR cc_start: 0.7621 (OUTLIER) cc_final: 0.7389 (t) outliers start: 22 outliers final: 19 residues processed: 50 average time/residue: 0.0360 time to fit residues: 2.1766 Evaluate side-chains 52 residues out of total 250 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 31 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 350 TYR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.0040 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.0270 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.2650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 493 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 = 0.3831 r_free = 0.3831 target = 0.162196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.136465 restraints weight = 2576.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.141853 restraints weight = 1294.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.145508 restraints weight = 818.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.147938 restraints weight = 598.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.149730 restraints weight = 477.662| |-----------------------------------------------------------------------------| r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2364 Z= 0.094 Angle : 0.491 6.957 3213 Z= 0.233 Chirality : 0.036 0.119 392 Planarity : 0.003 0.036 367 Dihedral : 10.316 156.861 306 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 5.20 % Allowed : 32.00 % Favored : 62.80 % 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: 3.08 (0.53), residues: 270 helix: 2.88 (0.36), residues: 204 sheet: -0.29 (1.49), residues: 10 loop : -0.88 (0.90), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 288 TYR 0.005 0.001 TYR A 436 PHE 0.010 0.001 PHE A 489 TRP 0.008 0.001 TRP A 490 HIS 0.001 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00187 ( 2364) covalent geometry : angle 0.49055 ( 3213) hydrogen bonds : bond 0.03551 ( 173) hydrogen bonds : angle 3.69694 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 486.65 seconds wall clock time: 9 minutes 1.85 seconds (541.85 seconds total)