Starting phenix.real_space_refine on Sat Apr 26 17:57:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xtw_38651/04_2025/8xtw_38651_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xtw_38651/04_2025/8xtw_38651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xtw_38651/04_2025/8xtw_38651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xtw_38651/04_2025/8xtw_38651.map" model { file = "/net/cci-nas-00/data/ceres_data/8xtw_38651/04_2025/8xtw_38651_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xtw_38651/04_2025/8xtw_38651_neut.cif" } resolution = 3.3 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= 0.000 sd= 0.034 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 17 5.16 5 C 1919 2.51 5 N 459 2.21 5 O 491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 2886 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2876 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 24, 'TRANS': 357} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Unusual residues: {'ACH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.02, per 1000 atoms: 1.05 Number of scatterers: 2886 At special positions: 0 Unit cell: (62.9, 68, 72.25, 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 17 16.00 O 491 8.00 N 459 7.00 C 1919 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: 0.68 Conformation dependent library (CDL) restraints added in 336.6 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 708 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 0 sheets defined 86.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 30 through 49 removed outlier: 4.553A pdb=" N LEU A 34 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 49 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 4.063A pdb=" N TYR A 60 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 61' Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.844A pdb=" N GLY A 125 " --> pdb=" O ASP A 121 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 147 removed outlier: 3.545A pdb=" N LEU A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Proline residue: A 140 - end of helix Proline residue: A 144 - end of helix removed outlier: 3.660A pdb=" N ASP A 147 " --> pdb=" O GLY A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 171 Processing helix chain 'A' and resid 175 through 204 removed outlier: 4.205A pdb=" N PHE A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASP A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR A 194 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 223 removed outlier: 3.716A pdb=" N SER A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ARG A 212 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 removed outlier: 4.388A pdb=" N PHE A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.676A pdb=" N PHE A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.535A pdb=" N ASP A 288 " --> pdb=" O ARG A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 301 Processing helix chain 'A' and resid 302 through 307 removed outlier: 3.550A pdb=" N ALA A 306 " --> pdb=" O ASN A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 352 removed outlier: 3.511A pdb=" N HIS A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 374 Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 379 through 412 removed outlier: 3.610A pdb=" N ALA A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) Proline residue: A 403 - end of helix removed outlier: 4.019A pdb=" N ALA A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 447 removed outlier: 4.127A pdb=" N ALA A 424 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA A 431 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix removed outlier: 5.751A pdb=" N GLY A 440 " --> pdb=" O PRO A 436 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N HIS A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 463 removed outlier: 3.679A pdb=" N LEU A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER A 452 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 470 removed outlier: 3.508A pdb=" N LEU A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 199 hydrogen bonds defined for protein. 588 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: 0.78 Time building geometry restraints manager: 0.81 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: 439 1.31 - 1.43: 769 1.43 - 1.56: 1720 1.56 - 1.68: 0 1.68 - 1.81: 28 Bond restraints: 2956 Sorted by residual: bond pdb=" C5 ACH A 701 " pdb=" O4 ACH A 701 " ideal model delta sigma weight residual 1.335 1.397 -0.062 2.00e-02 2.50e+03 9.74e+00 bond pdb=" CA ALA A 170 " pdb=" CB ALA A 170 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.55e-02 4.16e+03 8.07e+00 bond pdb=" C2 ACH A 701 " pdb=" N1 ACH A 701 " ideal model delta sigma weight residual 1.506 1.453 0.053 2.00e-02 2.50e+03 6.95e+00 bond pdb=" N LEU A 168 " pdb=" CA LEU A 168 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.18e-02 7.18e+03 6.39e+00 bond pdb=" N VAL A 167 " pdb=" CA VAL A 167 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.13e+00 ... (remaining 2951 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 3963 2.53 - 5.06: 67 5.06 - 7.59: 8 7.59 - 10.12: 2 10.12 - 12.64: 2 Bond angle restraints: 4042 Sorted by residual: angle pdb=" C ASP A 174 " pdb=" CA ASP A 174 " pdb=" CB ASP A 174 " ideal model delta sigma weight residual 115.89 107.34 8.55 1.32e+00 5.74e-01 4.19e+01 angle pdb=" C GLN A 31 " pdb=" CA GLN A 31 " pdb=" CB GLN A 31 " ideal model delta sigma weight residual 110.42 123.06 -12.64 1.99e+00 2.53e-01 4.04e+01 angle pdb=" C ALA A 170 " pdb=" N PHE A 171 " pdb=" CA PHE A 171 " ideal model delta sigma weight residual 122.62 111.58 11.04 1.78e+00 3.16e-01 3.85e+01 angle pdb=" C THR A 166 " pdb=" N VAL A 167 " pdb=" CA VAL A 167 " ideal model delta sigma weight residual 121.97 115.73 6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" C VAL A 374 " pdb=" CA VAL A 374 " pdb=" CB VAL A 374 " ideal model delta sigma weight residual 113.70 110.48 3.22 9.50e-01 1.11e+00 1.15e+01 ... (remaining 4037 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.46: 1412 13.46 - 26.91: 207 26.91 - 40.37: 85 40.37 - 53.82: 25 53.82 - 67.28: 4 Dihedral angle restraints: 1733 sinusoidal: 631 harmonic: 1102 Sorted by residual: dihedral pdb=" C GLN A 31 " pdb=" N GLN A 31 " pdb=" CA GLN A 31 " pdb=" CB GLN A 31 " ideal model delta harmonic sigma weight residual -122.60 -136.87 14.27 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" CA GLN A 31 " pdb=" C GLN A 31 " pdb=" N ARG A 32 " pdb=" CA ARG A 32 " ideal model delta harmonic sigma weight residual -180.00 -163.00 -17.00 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA SER A 150 " pdb=" C SER A 150 " pdb=" N TYR A 151 " pdb=" CA TYR A 151 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 1730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 465 0.085 - 0.171: 27 0.171 - 0.256: 0 0.256 - 0.342: 1 0.342 - 0.427: 1 Chirality restraints: 494 Sorted by residual: chirality pdb=" CA GLN A 31 " pdb=" N GLN A 31 " pdb=" C GLN A 31 " pdb=" CB GLN A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CA GLU A 173 " pdb=" N GLU A 173 " pdb=" C GLU A 173 " pdb=" CB GLU A 173 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA PHE A 169 " pdb=" N PHE A 169 " pdb=" C PHE A 169 " pdb=" CB PHE A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.97e-01 ... (remaining 491 not shown) Planarity restraints: 496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 352 " -0.047 5.00e-02 4.00e+02 7.22e-02 8.33e+00 pdb=" N PRO A 353 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 166 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.72e+00 pdb=" C THR A 166 " 0.045 2.00e-02 2.50e+03 pdb=" O THR A 166 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 167 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 463 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO A 464 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " -0.021 5.00e-02 4.00e+02 ... (remaining 493 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 887 2.82 - 3.34: 2739 3.34 - 3.86: 4621 3.86 - 4.38: 4830 4.38 - 4.90: 8754 Nonbonded interactions: 21831 Sorted by model distance: nonbonded pdb=" O SER A 415 " pdb=" OG SER A 415 " model vdw 2.302 3.040 nonbonded pdb=" O THR A 314 " pdb=" CD2 HIS A 318 " model vdw 2.325 3.260 nonbonded pdb=" OE1 GLN A 135 " pdb=" OG SER A 189 " model vdw 2.373 3.040 nonbonded pdb=" OG SER A 323 " pdb=" N GLU A 324 " model vdw 2.434 3.120 nonbonded pdb=" NE2 GLN A 135 " pdb=" OG SER A 429 " model vdw 2.435 3.120 ... (remaining 21826 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: 1.710 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.970 Find NCS groups from input model: 0.030 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.004 0.062 2956 Z= 0.221 Angle : 0.803 12.644 4042 Z= 0.455 Chirality : 0.047 0.427 494 Planarity : 0.006 0.072 496 Dihedral : 15.820 67.276 1025 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.33 % Allowed : 23.43 % Favored : 76.24 % Cbeta Deviations : 0.28 % 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: 0.29 (0.48), residues: 376 helix: 1.30 (0.35), residues: 279 sheet: None (None), residues: 0 loop : -3.23 (0.60), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 331 HIS 0.003 0.001 HIS A 354 PHE 0.009 0.001 PHE A 169 TYR 0.018 0.001 TYR A 175 ARG 0.002 0.000 ARG A 148 Details of bonding type rmsd hydrogen bonds : bond 0.18619 ( 199) hydrogen bonds : angle 5.65300 ( 588) covalent geometry : bond 0.00429 ( 2956) covalent geometry : angle 0.80328 ( 4042) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.287 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.1455 time to fit residues: 7.2373 Evaluate side-chains 31 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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: 0.7980 chunk 28 optimal weight: 0.0870 chunk 15 optimal weight: 0.0070 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.139865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.109201 restraints weight = 3531.442| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.52 r_work: 0.3040 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.1126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2956 Z= 0.131 Angle : 0.596 5.552 4042 Z= 0.301 Chirality : 0.039 0.121 494 Planarity : 0.006 0.058 496 Dihedral : 5.060 51.093 412 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.65 % Allowed : 23.76 % Favored : 74.59 % 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: 0.97 (0.48), residues: 376 helix: 1.87 (0.34), residues: 282 sheet: None (None), residues: 0 loop : -3.39 (0.59), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 331 HIS 0.011 0.002 HIS A 318 PHE 0.016 0.001 PHE A 169 TYR 0.011 0.001 TYR A 352 ARG 0.002 0.000 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.04543 ( 199) hydrogen bonds : angle 3.58353 ( 588) covalent geometry : bond 0.00294 ( 2956) covalent geometry : angle 0.59599 ( 4042) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.295 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 35 average time/residue: 0.1055 time to fit residues: 5.0778 Evaluate side-chains 34 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 6 optimal weight: 0.0010 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 15 optimal weight: 0.3980 chunk 30 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 = 0.3553 r_free = 0.3553 target = 0.139596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.108732 restraints weight = 3444.951| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.51 r_work: 0.3036 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2956 Z= 0.119 Angle : 0.553 5.680 4042 Z= 0.276 Chirality : 0.038 0.113 494 Planarity : 0.006 0.050 496 Dihedral : 4.790 47.959 412 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.30 % Allowed : 23.10 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.41 (0.48), residues: 376 helix: 2.17 (0.33), residues: 283 sheet: None (None), residues: 0 loop : -3.25 (0.61), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 331 HIS 0.003 0.001 HIS A 354 PHE 0.009 0.001 PHE A 169 TYR 0.008 0.001 TYR A 352 ARG 0.001 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03736 ( 199) hydrogen bonds : angle 3.30642 ( 588) covalent geometry : bond 0.00280 ( 2956) covalent geometry : angle 0.55334 ( 4042) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.287 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 34 average time/residue: 0.1068 time to fit residues: 4.9517 Evaluate side-chains 32 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 453 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 28 optimal weight: 0.0770 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.146106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.115831 restraints weight = 3444.715| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.49 r_work: 0.3003 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2956 Z= 0.128 Angle : 0.569 5.703 4042 Z= 0.282 Chirality : 0.039 0.120 494 Planarity : 0.006 0.045 496 Dihedral : 4.697 46.365 412 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.63 % Allowed : 23.43 % Favored : 72.94 % 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: 1.47 (0.48), residues: 376 helix: 2.24 (0.33), residues: 282 sheet: None (None), residues: 0 loop : -3.26 (0.61), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 331 HIS 0.004 0.001 HIS A 354 PHE 0.012 0.001 PHE A 169 TYR 0.007 0.001 TYR A 421 ARG 0.001 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 199) hydrogen bonds : angle 3.32146 ( 588) covalent geometry : bond 0.00310 ( 2956) covalent geometry : angle 0.56883 ( 4042) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.306 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 33 average time/residue: 0.1073 time to fit residues: 4.8952 Evaluate side-chains 36 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.145182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114814 restraints weight = 3533.527| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.53 r_work: 0.2995 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2956 Z= 0.135 Angle : 0.572 5.738 4042 Z= 0.283 Chirality : 0.039 0.120 494 Planarity : 0.006 0.041 496 Dihedral : 4.694 45.246 412 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.62 % Allowed : 22.77 % Favored : 72.61 % 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: 1.50 (0.48), residues: 376 helix: 2.25 (0.33), residues: 282 sheet: None (None), residues: 0 loop : -3.21 (0.60), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 331 HIS 0.004 0.001 HIS A 354 PHE 0.011 0.001 PHE A 169 TYR 0.007 0.001 TYR A 421 ARG 0.001 0.000 ARG A 378 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 199) hydrogen bonds : angle 3.30943 ( 588) covalent geometry : bond 0.00334 ( 2956) covalent geometry : angle 0.57177 ( 4042) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.262 Fit side-chains REVERT: A 385 VAL cc_start: 0.7967 (OUTLIER) cc_final: 0.7767 (t) outliers start: 14 outliers final: 9 residues processed: 41 average time/residue: 0.0967 time to fit residues: 5.3627 Evaluate side-chains 43 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.142642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.112268 restraints weight = 3583.204| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.54 r_work: 0.2945 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2956 Z= 0.152 Angle : 0.610 7.099 4042 Z= 0.299 Chirality : 0.040 0.151 494 Planarity : 0.006 0.041 496 Dihedral : 4.754 45.604 412 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.62 % Allowed : 23.10 % Favored : 72.28 % 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: 1.42 (0.48), residues: 376 helix: 2.12 (0.33), residues: 285 sheet: None (None), residues: 0 loop : -3.15 (0.62), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 331 HIS 0.004 0.001 HIS A 354 PHE 0.012 0.001 PHE A 169 TYR 0.009 0.001 TYR A 421 ARG 0.002 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.04454 ( 199) hydrogen bonds : angle 3.41348 ( 588) covalent geometry : bond 0.00384 ( 2956) covalent geometry : angle 0.60985 ( 4042) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 31 time to evaluate : 0.285 Fit side-chains outliers start: 14 outliers final: 11 residues processed: 37 average time/residue: 0.1018 time to fit residues: 5.1336 Evaluate side-chains 41 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 472 VAL 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 8 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 17 optimal weight: 0.0470 chunk 1 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.0020 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 overall best weight: 0.3686 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.145108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114598 restraints weight = 3588.146| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.55 r_work: 0.3007 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2956 Z= 0.116 Angle : 0.558 5.785 4042 Z= 0.272 Chirality : 0.038 0.115 494 Planarity : 0.005 0.041 496 Dihedral : 4.647 48.407 412 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.97 % Allowed : 23.43 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.76 (0.48), residues: 376 helix: 2.39 (0.33), residues: 284 sheet: None (None), residues: 0 loop : -3.07 (0.62), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 315 HIS 0.003 0.001 HIS A 354 PHE 0.007 0.001 PHE A 392 TYR 0.005 0.001 TYR A 421 ARG 0.001 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03347 ( 199) hydrogen bonds : angle 3.21811 ( 588) covalent geometry : bond 0.00274 ( 2956) covalent geometry : angle 0.55818 ( 4042) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.294 Fit side-chains REVERT: A 169 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.6887 (t80) REVERT: A 329 MET cc_start: 0.8414 (mtp) cc_final: 0.8209 (mtt) outliers start: 9 outliers final: 7 residues processed: 39 average time/residue: 0.1458 time to fit residues: 7.2309 Evaluate side-chains 40 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 37 optimal weight: 0.0170 chunk 5 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 27 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 overall best weight: 0.4218 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.144923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.114357 restraints weight = 3559.448| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.55 r_work: 0.2998 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2956 Z= 0.116 Angle : 0.560 6.111 4042 Z= 0.272 Chirality : 0.039 0.117 494 Planarity : 0.005 0.041 496 Dihedral : 4.556 48.461 412 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.97 % Allowed : 23.10 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.94 (0.48), residues: 376 helix: 2.39 (0.33), residues: 289 sheet: None (None), residues: 0 loop : -2.81 (0.64), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 315 HIS 0.003 0.001 HIS A 354 PHE 0.007 0.001 PHE A 169 TYR 0.006 0.001 TYR A 421 ARG 0.004 0.000 ARG A 351 Details of bonding type rmsd hydrogen bonds : bond 0.03419 ( 199) hydrogen bonds : angle 3.18915 ( 588) covalent geometry : bond 0.00277 ( 2956) covalent geometry : angle 0.56014 ( 4042) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.315 Fit side-chains REVERT: A 169 PHE cc_start: 0.7895 (OUTLIER) cc_final: 0.6892 (t80) REVERT: A 329 MET cc_start: 0.8423 (mtp) cc_final: 0.8192 (mtt) outliers start: 9 outliers final: 8 residues processed: 38 average time/residue: 0.1207 time to fit residues: 5.9840 Evaluate side-chains 43 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.0040 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 overall best weight: 0.6192 ------------------------------------------------------------------------------- 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 = 0.3623 r_free = 0.3623 target = 0.142920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.112290 restraints weight = 3535.505| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 2.55 r_work: 0.2968 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2956 Z= 0.130 Angle : 0.574 6.157 4042 Z= 0.280 Chirality : 0.039 0.118 494 Planarity : 0.005 0.041 496 Dihedral : 4.576 48.232 412 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.30 % Allowed : 22.77 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.91 (0.48), residues: 376 helix: 2.32 (0.33), residues: 290 sheet: None (None), residues: 0 loop : -2.65 (0.65), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 331 HIS 0.003 0.001 HIS A 354 PHE 0.010 0.001 PHE A 169 TYR 0.008 0.001 TYR A 421 ARG 0.004 0.000 ARG A 351 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 199) hydrogen bonds : angle 3.24625 ( 588) covalent geometry : bond 0.00322 ( 2956) covalent geometry : angle 0.57436 ( 4042) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.316 Fit side-chains REVERT: A 169 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.6826 (t80) outliers start: 10 outliers final: 9 residues processed: 38 average time/residue: 0.1164 time to fit residues: 5.8139 Evaluate side-chains 44 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3489 r_free = 0.3489 target = 0.134232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.103149 restraints weight = 3587.996| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.52 r_work: 0.2967 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2956 Z= 0.128 Angle : 0.570 5.970 4042 Z= 0.279 Chirality : 0.039 0.119 494 Planarity : 0.005 0.041 496 Dihedral : 4.585 48.936 412 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.63 % Allowed : 22.77 % Favored : 73.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.92 (0.48), residues: 376 helix: 2.33 (0.33), residues: 290 sheet: None (None), residues: 0 loop : -2.66 (0.65), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 357 HIS 0.003 0.001 HIS A 354 PHE 0.009 0.001 PHE A 169 TYR 0.007 0.001 TYR A 421 ARG 0.004 0.000 ARG A 351 Details of bonding type rmsd hydrogen bonds : bond 0.03843 ( 199) hydrogen bonds : angle 3.23502 ( 588) covalent geometry : bond 0.00316 ( 2956) covalent geometry : angle 0.56999 ( 4042) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.241 Fit side-chains REVERT: A 169 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6711 (t80) outliers start: 11 outliers final: 10 residues processed: 39 average time/residue: 0.1203 time to fit residues: 6.0569 Evaluate side-chains 46 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 PHE Chi-restraints excluded: chain A residue 283 HIS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain A residue 472 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3466 r_free = 0.3466 target = 0.132163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101865 restraints weight = 3503.071| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.42 r_work: 0.2980 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2956 Z= 0.138 Angle : 0.582 6.266 4042 Z= 0.285 Chirality : 0.040 0.119 494 Planarity : 0.006 0.041 496 Dihedral : 4.608 49.534 412 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.63 % Allowed : 23.10 % Favored : 73.27 % 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: 1.85 (0.48), residues: 376 helix: 2.29 (0.33), residues: 289 sheet: None (None), residues: 0 loop : -2.69 (0.64), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 331 HIS 0.003 0.001 HIS A 354 PHE 0.010 0.001 PHE A 169 TYR 0.008 0.001 TYR A 421 ARG 0.004 0.000 ARG A 351 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 199) hydrogen bonds : angle 3.27866 ( 588) covalent geometry : bond 0.00347 ( 2956) covalent geometry : angle 0.58168 ( 4042) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.19 seconds wall clock time: 27 minutes 58.64 seconds (1678.64 seconds total)