Starting phenix.real_space_refine on Mon Feb 10 21:42:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wlk_37622/02_2025/8wlk_37622.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wlk_37622/02_2025/8wlk_37622.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wlk_37622/02_2025/8wlk_37622.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wlk_37622/02_2025/8wlk_37622.map" model { file = "/net/cci-nas-00/data/ceres_data/8wlk_37622/02_2025/8wlk_37622.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wlk_37622/02_2025/8wlk_37622.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.094 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 24 5.16 5 C 1918 2.51 5 N 445 2.21 5 O 486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2873 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2850 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'EBZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.41, per 1000 atoms: 0.84 Number of scatterers: 2873 At special positions: 0 Unit cell: (58.716, 74.56, 69.9, 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 24 16.00 O 486 8.00 N 445 7.00 C 1918 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: 0.82 Conformation dependent library (CDL) restraints added in 348.2 milliseconds 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 690 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 86.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.601A pdb=" N ILE A 22 " --> pdb=" O SER A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 128 through 157 removed outlier: 4.610A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix Processing helix chain 'A' and resid 158 through 178 removed outlier: 3.924A pdb=" N PHE A 178 " --> pdb=" O ILE A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.817A pdb=" N GLY A 218 " --> pdb=" O ASP A 214 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN A 219 " --> pdb=" O GLU A 215 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.670A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 291 through 310 Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 334 through 356 removed outlier: 5.456A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 384 through 414 removed outlier: 3.954A pdb=" N ASN A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 389 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 393 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Proline residue: A 404 - end of helix removed outlier: 3.876A pdb=" N VAL A 410 " --> pdb=" O MET A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 447 removed outlier: 4.182A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 238 hydrogen bonds defined for protein. 690 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: 0.85 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 434 1.31 - 1.44: 761 1.44 - 1.56: 1705 1.56 - 1.69: 2 1.69 - 1.81: 41 Bond restraints: 2943 Sorted by residual: bond pdb=" C05 EBZ A 501 " pdb=" N04 EBZ A 501 " ideal model delta sigma weight residual 1.460 1.385 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C06 EBZ A 501 " pdb=" C07 EBZ A 501 " ideal model delta sigma weight residual 1.392 1.317 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" C12 EBZ A 501 " pdb=" C14 EBZ A 501 " ideal model delta sigma weight residual 1.525 1.592 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C12 EBZ A 501 " pdb=" N04 EBZ A 501 " ideal model delta sigma weight residual 1.452 1.391 0.061 2.00e-02 2.50e+03 9.38e+00 bond pdb=" C07 EBZ A 501 " pdb=" C14 EBZ A 501 " ideal model delta sigma weight residual 1.512 1.570 -0.058 2.00e-02 2.50e+03 8.51e+00 ... (remaining 2938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 3882 2.09 - 4.18: 89 4.18 - 6.28: 28 6.28 - 8.37: 9 8.37 - 10.46: 3 Bond angle restraints: 4011 Sorted by residual: angle pdb=" N ASN A 146 " pdb=" CA ASN A 146 " pdb=" C ASN A 146 " ideal model delta sigma weight residual 109.81 116.67 -6.86 2.21e+00 2.05e-01 9.62e+00 angle pdb=" CA LEU A 152 " pdb=" CB LEU A 152 " pdb=" CG LEU A 152 " ideal model delta sigma weight residual 116.30 126.76 -10.46 3.50e+00 8.16e-02 8.93e+00 angle pdb=" C06 EBZ A 501 " pdb=" C05 EBZ A 501 " pdb=" C08 EBZ A 501 " ideal model delta sigma weight residual 115.53 106.85 8.68 3.00e+00 1.11e-01 8.37e+00 angle pdb=" CA PRO A 45 " pdb=" N PRO A 45 " pdb=" CD PRO A 45 " ideal model delta sigma weight residual 112.00 107.99 4.01 1.40e+00 5.10e-01 8.22e+00 angle pdb=" N TYR A 158 " pdb=" CA TYR A 158 " pdb=" C TYR A 158 " ideal model delta sigma weight residual 109.81 116.12 -6.31 2.21e+00 2.05e-01 8.14e+00 ... (remaining 4006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.64: 1671 28.64 - 57.28: 58 57.28 - 85.91: 8 85.91 - 114.55: 3 114.55 - 143.19: 1 Dihedral angle restraints: 1741 sinusoidal: 658 harmonic: 1083 Sorted by residual: dihedral pdb=" C13 EBZ A 501 " pdb=" C18 EBZ A 501 " pdb=" C19 EBZ A 501 " pdb=" C23 EBZ A 501 " ideal model delta sinusoidal sigma weight residual 59.15 -157.66 -143.19 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C13 EBZ A 501 " pdb=" C18 EBZ A 501 " pdb=" C19 EBZ A 501 " pdb=" C22 EBZ A 501 " ideal model delta sinusoidal sigma weight residual 182.76 79.21 103.55 1 3.00e+01 1.11e-03 1.32e+01 dihedral pdb=" CA ILE A 395 " pdb=" C ILE A 395 " pdb=" N GLY A 396 " pdb=" CA GLY A 396 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 1738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 325 0.044 - 0.087: 113 0.087 - 0.131: 35 0.131 - 0.174: 6 0.174 - 0.217: 2 Chirality restraints: 481 Sorted by residual: chirality pdb=" C05 EBZ A 501 " pdb=" C06 EBZ A 501 " pdb=" C08 EBZ A 501 " pdb=" N04 EBZ A 501 " both_signs ideal model delta sigma weight residual False 2.38 2.16 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB VAL A 427 " pdb=" CA VAL A 427 " pdb=" CG1 VAL A 427 " pdb=" CG2 VAL A 427 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ILE A 317 " pdb=" N ILE A 317 " pdb=" C ILE A 317 " pdb=" CB ILE A 317 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.18e-01 ... (remaining 478 not shown) Planarity restraints: 492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 44 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO A 45 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO A 45 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 45 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 468 " -0.010 2.00e-02 2.50e+03 1.62e-02 4.57e+00 pdb=" CG PHE A 468 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 468 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 468 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE A 468 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 468 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 468 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " -0.028 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 161 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " -0.023 5.00e-02 4.00e+02 ... (remaining 489 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 506 2.76 - 3.30: 3017 3.30 - 3.83: 4935 3.83 - 4.37: 5411 4.37 - 4.90: 9537 Nonbonded interactions: 23406 Sorted by model distance: nonbonded pdb=" NE2 GLN A 142 " pdb=" OD2 ASP A 426 " model vdw 2.227 3.120 nonbonded pdb=" O MET A 175 " pdb=" OG SER A 179 " model vdw 2.273 3.040 nonbonded pdb=" O ILE A 194 " pdb=" OG SER A 197 " model vdw 2.310 3.040 nonbonded pdb=" OG SER A 273 " pdb=" NH1 ARG A 274 " model vdw 2.346 3.120 nonbonded pdb=" OH TYR A 341 " pdb=" OD2 ASP A 399 " model vdw 2.381 3.040 ... (remaining 23401 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: 0.440 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 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 0.075 2943 Z= 0.367 Angle : 0.907 10.461 4011 Z= 0.424 Chirality : 0.049 0.217 481 Planarity : 0.007 0.107 492 Dihedral : 15.662 143.186 1051 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.43), residues: 379 helix: 0.53 (0.30), residues: 295 sheet: None (None), residues: 0 loop : -1.68 (0.68), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.001 0.001 HIS A 414 PHE 0.036 0.002 PHE A 468 TYR 0.008 0.001 TYR A 422 ARG 0.006 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.310 Fit side-chains REVERT: A 291 ASP cc_start: 0.8884 (t70) cc_final: 0.8383 (t0) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.1117 time to fit residues: 14.4999 Evaluate side-chains 92 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 0.0270 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 = 0.4111 r_free = 0.4111 target = 0.179248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.162053 restraints weight = 4205.250| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 3.23 r_work: 0.3793 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2943 Z= 0.207 Angle : 0.703 7.374 4011 Z= 0.343 Chirality : 0.043 0.175 481 Planarity : 0.006 0.068 492 Dihedral : 11.335 140.734 435 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.66 % Allowed : 17.28 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.44), residues: 379 helix: 0.87 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -1.55 (0.72), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.020 0.002 PHE A 468 TYR 0.011 0.001 TYR A 341 ARG 0.002 0.000 ARG A 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.376 Fit side-chains REVERT: A 397 MET cc_start: 0.7696 (mmp) cc_final: 0.7479 (mmt) REVERT: A 453 MET cc_start: 0.6864 (mmp) cc_final: 0.6328 (mmp) outliers start: 8 outliers final: 6 residues processed: 95 average time/residue: 0.1059 time to fit residues: 12.8750 Evaluate side-chains 92 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.173817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.157669 restraints weight = 4150.808| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 3.18 r_work: 0.3750 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2943 Z= 0.232 Angle : 0.667 6.048 4011 Z= 0.331 Chirality : 0.043 0.172 481 Planarity : 0.005 0.055 492 Dihedral : 10.840 130.294 435 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 4.65 % Allowed : 22.59 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.44), residues: 379 helix: 1.13 (0.30), residues: 297 sheet: None (None), residues: 0 loop : -1.51 (0.72), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.015 0.001 PHE A 429 TYR 0.012 0.001 TYR A 341 ARG 0.004 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.311 Fit side-chains REVERT: A 152 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7094 (mp) REVERT: A 308 ILE cc_start: 0.6334 (OUTLIER) cc_final: 0.5759 (mm) REVERT: A 347 ILE cc_start: 0.7347 (tp) cc_final: 0.7073 (tp) REVERT: A 397 MET cc_start: 0.7636 (mmp) cc_final: 0.7414 (mmp) outliers start: 14 outliers final: 7 residues processed: 99 average time/residue: 0.0946 time to fit residues: 12.2561 Evaluate side-chains 99 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 90 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.167645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151475 restraints weight = 4304.800| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 3.16 r_work: 0.3686 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 2943 Z= 0.296 Angle : 0.674 6.242 4011 Z= 0.339 Chirality : 0.044 0.139 481 Planarity : 0.005 0.049 492 Dihedral : 10.751 123.159 435 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.65 % Allowed : 24.25 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.44), residues: 379 helix: 1.20 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -1.59 (0.70), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 318 HIS 0.004 0.002 HIS A 353 PHE 0.021 0.002 PHE A 429 TYR 0.015 0.001 TYR A 341 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.298 Fit side-chains REVERT: A 152 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7154 (mp) REVERT: A 308 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6577 (mm) REVERT: A 341 TYR cc_start: 0.8478 (t80) cc_final: 0.8271 (t80) REVERT: A 346 ASN cc_start: 0.8688 (m110) cc_final: 0.8476 (m110) REVERT: A 347 ILE cc_start: 0.7611 (tp) cc_final: 0.7322 (tp) REVERT: A 453 MET cc_start: 0.7577 (mmm) cc_final: 0.7292 (mmp) outliers start: 17 outliers final: 9 residues processed: 104 average time/residue: 0.0903 time to fit residues: 12.3021 Evaluate side-chains 104 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.169110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.153388 restraints weight = 4218.197| |-----------------------------------------------------------------------------| r_work (start): 0.3831 rms_B_bonded: 3.11 r_work: 0.3710 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 2943 Z= 0.243 Angle : 0.680 10.319 4011 Z= 0.335 Chirality : 0.042 0.132 481 Planarity : 0.005 0.043 492 Dihedral : 10.556 123.902 435 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.98 % Allowed : 24.25 % Favored : 69.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.44), residues: 379 helix: 1.29 (0.30), residues: 296 sheet: None (None), residues: 0 loop : -1.60 (0.70), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 318 HIS 0.004 0.002 HIS A 353 PHE 0.014 0.001 PHE A 429 TYR 0.011 0.001 TYR A 341 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.304 Fit side-chains REVERT: A 152 LEU cc_start: 0.7801 (OUTLIER) cc_final: 0.7391 (tp) REVERT: A 271 GLN cc_start: 0.7491 (tt0) cc_final: 0.7188 (tt0) REVERT: A 308 ILE cc_start: 0.6790 (OUTLIER) cc_final: 0.6500 (mm) REVERT: A 347 ILE cc_start: 0.7444 (tp) cc_final: 0.7173 (tp) REVERT: A 449 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.6808 (t80) REVERT: A 453 MET cc_start: 0.7674 (mmm) cc_final: 0.7344 (mmp) outliers start: 18 outliers final: 11 residues processed: 104 average time/residue: 0.0945 time to fit residues: 12.8461 Evaluate side-chains 104 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 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 = 0.4010 r_free = 0.4010 target = 0.168814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.153006 restraints weight = 4307.469| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 3.15 r_work: 0.3707 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2943 Z= 0.224 Angle : 0.708 9.196 4011 Z= 0.346 Chirality : 0.043 0.191 481 Planarity : 0.005 0.040 492 Dihedral : 10.377 124.140 435 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.65 % Allowed : 24.92 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.43), residues: 379 helix: 1.21 (0.29), residues: 297 sheet: None (None), residues: 0 loop : -1.49 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.003 0.001 HIS A 353 PHE 0.013 0.001 PHE A 429 TYR 0.010 0.001 TYR A 341 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.283 Fit side-chains REVERT: A 152 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7185 (mp) REVERT: A 221 MET cc_start: 0.8075 (mmm) cc_final: 0.7586 (mtp) REVERT: A 271 GLN cc_start: 0.7509 (tt0) cc_final: 0.7177 (tt0) REVERT: A 295 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8197 (mm) REVERT: A 347 ILE cc_start: 0.7328 (tp) cc_final: 0.7079 (tp) REVERT: A 449 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.6775 (t80) REVERT: A 453 MET cc_start: 0.7733 (mmm) cc_final: 0.7379 (mmp) outliers start: 17 outliers final: 12 residues processed: 100 average time/residue: 0.1065 time to fit residues: 13.6516 Evaluate side-chains 101 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.0570 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 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 = 0.4016 r_free = 0.4016 target = 0.169520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153624 restraints weight = 4328.326| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 3.17 r_work: 0.3709 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2943 Z= 0.217 Angle : 0.694 8.452 4011 Z= 0.338 Chirality : 0.043 0.192 481 Planarity : 0.005 0.040 492 Dihedral : 10.288 125.237 435 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.98 % Allowed : 25.91 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.43), residues: 379 helix: 1.21 (0.29), residues: 297 sheet: None (None), residues: 0 loop : -1.48 (0.71), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.003 0.002 HIS A 353 PHE 0.013 0.001 PHE A 27 TYR 0.007 0.001 TYR A 422 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.320 Fit side-chains REVERT: A 152 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7163 (mp) REVERT: A 221 MET cc_start: 0.8015 (mmm) cc_final: 0.7469 (mtp) REVERT: A 271 GLN cc_start: 0.7466 (tt0) cc_final: 0.7123 (tt0) REVERT: A 295 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 449 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.6843 (t80) outliers start: 18 outliers final: 14 residues processed: 100 average time/residue: 0.0948 time to fit residues: 12.4563 Evaluate side-chains 104 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 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 = 0.4013 r_free = 0.4013 target = 0.169100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.153308 restraints weight = 4280.728| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 3.14 r_work: 0.3707 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2943 Z= 0.231 Angle : 0.693 8.174 4011 Z= 0.339 Chirality : 0.043 0.193 481 Planarity : 0.005 0.040 492 Dihedral : 10.285 127.237 435 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 6.64 % Allowed : 26.25 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.43), residues: 379 helix: 1.16 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -1.45 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.003 0.001 HIS A 353 PHE 0.026 0.002 PHE A 468 TYR 0.008 0.001 TYR A 422 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.324 Fit side-chains REVERT: A 152 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7349 (tp) REVERT: A 221 MET cc_start: 0.8099 (mmm) cc_final: 0.7544 (mtp) REVERT: A 295 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8140 (mm) REVERT: A 449 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.6597 (t80) REVERT: A 453 MET cc_start: 0.7826 (mmm) cc_final: 0.7243 (mmm) outliers start: 20 outliers final: 16 residues processed: 99 average time/residue: 0.0979 time to fit residues: 12.6333 Evaluate side-chains 105 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 451 TRP Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 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 = 0.4007 r_free = 0.4007 target = 0.168378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.152564 restraints weight = 4288.464| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.13 r_work: 0.3703 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2943 Z= 0.246 Angle : 0.720 9.517 4011 Z= 0.348 Chirality : 0.043 0.190 481 Planarity : 0.005 0.040 492 Dihedral : 10.258 127.796 435 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 6.64 % Allowed : 26.58 % Favored : 66.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.43), residues: 379 helix: 1.13 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -1.50 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.003 0.001 HIS A 353 PHE 0.016 0.002 PHE A 135 TYR 0.010 0.001 TYR A 422 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.251 Fit side-chains REVERT: A 152 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7334 (tp) REVERT: A 221 MET cc_start: 0.8125 (mmm) cc_final: 0.7703 (mtp) REVERT: A 271 GLN cc_start: 0.7466 (tt0) cc_final: 0.7134 (tt0) REVERT: A 295 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8159 (mm) REVERT: A 449 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.6856 (t80) REVERT: A 453 MET cc_start: 0.7889 (mmm) cc_final: 0.7451 (mmp) outliers start: 20 outliers final: 14 residues processed: 99 average time/residue: 0.0914 time to fit residues: 11.8075 Evaluate side-chains 104 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 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 = 0.4006 r_free = 0.4006 target = 0.168537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152693 restraints weight = 4324.761| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.15 r_work: 0.3701 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2943 Z= 0.241 Angle : 0.715 9.440 4011 Z= 0.348 Chirality : 0.043 0.190 481 Planarity : 0.005 0.040 492 Dihedral : 10.263 124.265 435 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 5.98 % Allowed : 26.25 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.43), residues: 379 helix: 1.17 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -1.49 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.002 0.001 HIS A 353 PHE 0.016 0.002 PHE A 27 TYR 0.011 0.001 TYR A 422 ARG 0.005 0.000 ARG A 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 758 Ramachandran restraints generated. 379 Oldfield, 0 Emsley, 379 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.301 Fit side-chains REVERT: A 152 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7336 (tp) REVERT: A 221 MET cc_start: 0.8080 (mmm) cc_final: 0.7691 (mtp) REVERT: A 271 GLN cc_start: 0.7485 (tt0) cc_final: 0.7162 (tt0) REVERT: A 295 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8165 (mm) REVERT: A 449 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.6908 (t80) outliers start: 18 outliers final: 15 residues processed: 99 average time/residue: 0.0915 time to fit residues: 11.8315 Evaluate side-chains 106 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 384 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 410 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 449 PHE Chi-restraints excluded: chain A residue 451 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 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 = 0.4001 r_free = 0.4001 target = 0.167974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152071 restraints weight = 4230.126| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.13 r_work: 0.3696 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 2943 Z= 0.245 Angle : 0.716 9.473 4011 Z= 0.349 Chirality : 0.043 0.187 481 Planarity : 0.005 0.040 492 Dihedral : 10.236 124.674 435 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 6.31 % Allowed : 26.25 % Favored : 67.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.43), residues: 379 helix: 1.19 (0.29), residues: 298 sheet: None (None), residues: 0 loop : -1.51 (0.71), residues: 81 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 318 HIS 0.003 0.002 HIS A 353 PHE 0.014 0.002 PHE A 27 TYR 0.011 0.001 TYR A 422 ARG 0.005 0.000 ARG A 357 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1405.59 seconds wall clock time: 26 minutes 6.96 seconds (1566.96 seconds total)