Starting phenix.real_space_refine on Fri Dec 27 09:38:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tej_41188/12_2024/8tej_41188.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tej_41188/12_2024/8tej_41188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tej_41188/12_2024/8tej_41188.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tej_41188/12_2024/8tej_41188.map" model { file = "/net/cci-nas-00/data/ceres_data/8tej_41188/12_2024/8tej_41188.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tej_41188/12_2024/8tej_41188.cif" } resolution = 2.55 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 26 5.16 5 C 2555 2.51 5 N 645 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3925 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3903 Classifications: {'peptide': 494} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 467} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 3.44, per 1000 atoms: 0.88 Number of scatterers: 3925 At special positions: 0 Unit cell: (64.74, 78.02, 93.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 26 16.00 P 1 15.00 O 698 8.00 N 645 7.00 C 2555 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: 1.11 Conformation dependent library (CDL) restraints added in 488.1 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 77.9% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 21 through 32 removed outlier: 3.671A pdb=" N ALA A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 36 through 62 Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 67 through 86 Processing helix chain 'A' and resid 96 through 112 removed outlier: 3.633A pdb=" N ALA A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 142 Processing helix chain 'A' and resid 145 through 151 removed outlier: 4.172A pdb=" N ASN A 149 " --> pdb=" O CYS A 145 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 151 " --> pdb=" O ILE A 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 151' Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.681A pdb=" N GLY A 156 " --> pdb=" O THR A 152 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 193 through 219 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 228 through 251 removed outlier: 6.277A pdb=" N VAL A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Proline residue: A 241 - end of helix Processing helix chain 'A' and resid 252 through 257 removed outlier: 4.447A pdb=" N GLY A 256 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 287 removed outlier: 3.730A pdb=" N LEU A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 297 Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.540A pdb=" N SER A 313 " --> pdb=" O TYR A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'A' and resid 359 through 391 removed outlier: 3.706A pdb=" N LYS A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 Processing helix chain 'A' and resid 424 through 431 removed outlier: 3.524A pdb=" N THR A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 4.379A pdb=" N ASP A 453 " --> pdb=" O GLU A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 456 No H-bonds generated for 'chain 'A' and resid 454 through 456' Processing helix chain 'A' and resid 464 through 477 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 488 through 503 removed outlier: 3.721A pdb=" N LEU A 492 " --> pdb=" O PRO A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 516 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 94 259 hydrogen bonds defined for protein. 753 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: 1.06 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1209 1.34 - 1.46: 574 1.46 - 1.57: 2168 1.57 - 1.69: 3 1.69 - 1.81: 45 Bond restraints: 3999 Sorted by residual: bond pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.717 1.609 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" O3P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb=" O2P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.528 1.607 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O1P TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 1.525 1.479 0.046 2.00e-02 2.50e+03 5.35e+00 bond pdb=" N TPO A 410 " pdb=" CA TPO A 410 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.83e+00 ... (remaining 3994 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 5374 2.30 - 4.60: 47 4.60 - 6.90: 3 6.90 - 9.20: 0 9.20 - 11.50: 2 Bond angle restraints: 5426 Sorted by residual: angle pdb=" CB TPO A 410 " pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " ideal model delta sigma weight residual 119.31 107.81 11.50 3.00e+00 1.11e-01 1.47e+01 angle pdb=" OG1 TPO A 410 " pdb=" P TPO A 410 " pdb=" O1P TPO A 410 " ideal model delta sigma weight residual 100.43 110.03 -9.60 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C PRO A 7 " pdb=" N PHE A 8 " pdb=" CA PHE A 8 " ideal model delta sigma weight residual 121.54 125.90 -4.36 1.91e+00 2.74e-01 5.21e+00 angle pdb=" N GLY A 395 " pdb=" CA GLY A 395 " pdb=" C GLY A 395 " ideal model delta sigma weight residual 113.18 108.47 4.71 2.37e+00 1.78e-01 3.95e+00 angle pdb=" O1P TPO A 410 " pdb=" P TPO A 410 " pdb=" O3P TPO A 410 " ideal model delta sigma weight residual 115.11 109.22 5.89 3.00e+00 1.11e-01 3.85e+00 ... (remaining 5421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 1995 16.02 - 32.04: 245 32.04 - 48.06: 82 48.06 - 64.08: 36 64.08 - 80.10: 7 Dihedral angle restraints: 2365 sinusoidal: 946 harmonic: 1419 Sorted by residual: dihedral pdb=" CA ILE A 291 " pdb=" C ILE A 291 " pdb=" N VAL A 292 " pdb=" CA VAL A 292 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLY A 395 " pdb=" C GLY A 395 " pdb=" N GLN A 396 " pdb=" CA GLN A 396 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA ILE A 295 " pdb=" CB ILE A 295 " pdb=" CG1 ILE A 295 " pdb=" CD1 ILE A 295 " ideal model delta sinusoidal sigma weight residual 60.00 119.76 -59.76 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 2362 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 396 0.026 - 0.052: 128 0.052 - 0.079: 62 0.079 - 0.105: 19 0.105 - 0.131: 11 Chirality restraints: 616 Sorted by residual: chirality pdb=" CA ILE A 181 " pdb=" N ILE A 181 " pdb=" C ILE A 181 " pdb=" CB ILE A 181 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.30e-01 chirality pdb=" CA VAL A 289 " pdb=" N VAL A 289 " pdb=" C VAL A 289 " pdb=" CB VAL A 289 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA ILE A 92 " pdb=" N ILE A 92 " pdb=" C ILE A 92 " pdb=" CB ILE A 92 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 613 not shown) Planarity restraints: 674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 247 " 0.005 2.00e-02 2.50e+03 9.47e-03 8.96e-01 pdb=" C TRP A 247 " -0.016 2.00e-02 2.50e+03 pdb=" O TRP A 247 " 0.006 2.00e-02 2.50e+03 pdb=" N THR A 248 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 258 " -0.015 5.00e-02 4.00e+02 2.22e-02 7.86e-01 pdb=" N PRO A 259 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 361 " -0.014 5.00e-02 4.00e+02 2.14e-02 7.30e-01 pdb=" N PRO A 362 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " -0.012 5.00e-02 4.00e+02 ... (remaining 671 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 25 2.57 - 3.15: 3166 3.15 - 3.73: 6231 3.73 - 4.32: 8524 4.32 - 4.90: 14206 Nonbonded interactions: 32152 Sorted by model distance: nonbonded pdb=" OH TYR A 405 " pdb=" OE2 GLU A 459 " model vdw 1.984 3.040 nonbonded pdb=" OD2 ASP A 335 " pdb=" O HOH A 801 " model vdw 2.033 3.040 nonbonded pdb=" OH TYR A 22 " pdb=" O ILE A 84 " model vdw 2.042 3.040 nonbonded pdb=" O GLY A 261 " pdb=" O HOH A 802 " model vdw 2.085 3.040 nonbonded pdb=" O LYS A 424 " pdb=" OG1 THR A 427 " model vdw 2.171 3.040 ... (remaining 32147 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.220 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 0.108 3999 Z= 0.251 Angle : 0.572 11.496 5426 Z= 0.276 Chirality : 0.036 0.131 616 Planarity : 0.003 0.027 674 Dihedral : 17.726 80.101 1453 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 20.57 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.14 (0.38), residues: 485 helix: 2.11 (0.28), residues: 336 sheet: None (None), residues: 0 loop : -0.15 (0.51), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.006 0.001 PHE A 107 TYR 0.011 0.001 TYR A 495 ARG 0.005 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.448 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 1.2956 time to fit residues: 73.8292 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3999 Z= 0.194 Angle : 0.511 5.634 5426 Z= 0.260 Chirality : 0.039 0.168 616 Planarity : 0.004 0.032 674 Dihedral : 6.187 43.322 547 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 17.94 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.15 (0.37), residues: 485 helix: 2.09 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -0.14 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 131 HIS 0.003 0.001 HIS A 312 PHE 0.009 0.001 PHE A 509 TYR 0.012 0.001 TYR A 495 ARG 0.003 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.453 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 57 average time/residue: 1.3564 time to fit residues: 80.0679 Evaluate side-chains 47 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3999 Z= 0.166 Angle : 0.483 5.578 5426 Z= 0.244 Chirality : 0.038 0.159 616 Planarity : 0.004 0.033 674 Dihedral : 5.201 36.040 538 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.83 % Allowed : 18.90 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.28 (0.37), residues: 485 helix: 2.19 (0.27), residues: 338 sheet: None (None), residues: 0 loop : -0.07 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 131 HIS 0.003 0.001 HIS A 312 PHE 0.008 0.001 PHE A 509 TYR 0.011 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.440 Fit side-chains REVERT: A 35 ARG cc_start: 0.7301 (mtt180) cc_final: 0.6716 (mpp-170) REVERT: A 219 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8412 (mmm160) REVERT: A 295 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8163 (mp) outliers start: 16 outliers final: 6 residues processed: 61 average time/residue: 1.2995 time to fit residues: 82.0173 Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 0.0980 chunk 26 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3999 Z= 0.160 Angle : 0.474 5.577 5426 Z= 0.241 Chirality : 0.038 0.164 616 Planarity : 0.004 0.032 674 Dihedral : 5.069 34.923 538 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.11 % Allowed : 19.86 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.36 (0.37), residues: 485 helix: 2.25 (0.27), residues: 338 sheet: None (None), residues: 0 loop : -0.02 (0.50), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.006 0.001 PHE A 509 TYR 0.012 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.410 Fit side-chains REVERT: A 35 ARG cc_start: 0.7318 (mtt180) cc_final: 0.6723 (mpp-170) REVERT: A 181 ILE cc_start: 0.6655 (OUTLIER) cc_final: 0.5795 (mt) REVERT: A 219 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8412 (mmm160) REVERT: A 295 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8147 (mp) outliers start: 13 outliers final: 6 residues processed: 57 average time/residue: 1.2599 time to fit residues: 74.4232 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 502 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3999 Z= 0.191 Angle : 0.509 7.224 5426 Z= 0.256 Chirality : 0.039 0.160 616 Planarity : 0.004 0.032 674 Dihedral : 4.802 35.552 536 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.11 % Allowed : 20.57 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.22 (0.37), residues: 485 helix: 2.13 (0.27), residues: 339 sheet: None (None), residues: 0 loop : -0.04 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.003 0.001 HIS A 312 PHE 0.008 0.001 PHE A 509 TYR 0.013 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.434 Fit side-chains REVERT: A 16 LYS cc_start: 0.7436 (mtpp) cc_final: 0.7085 (pttp) REVERT: A 219 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8412 (mmm160) REVERT: A 295 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8174 (mp) REVERT: A 463 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.7611 (pp30) outliers start: 13 outliers final: 6 residues processed: 57 average time/residue: 1.2946 time to fit residues: 76.4697 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3999 Z= 0.192 Angle : 0.510 6.379 5426 Z= 0.257 Chirality : 0.039 0.162 616 Planarity : 0.004 0.032 674 Dihedral : 4.742 36.316 535 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.87 % Allowed : 20.57 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.17 (0.37), residues: 485 helix: 2.12 (0.28), residues: 333 sheet: None (None), residues: 0 loop : -0.05 (0.49), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.008 0.001 PHE A 509 TYR 0.013 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.453 Fit side-chains REVERT: A 16 LYS cc_start: 0.7443 (mtpp) cc_final: 0.7091 (pttp) REVERT: A 115 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.5587 (mp0) REVERT: A 219 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8415 (mmm160) REVERT: A 295 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8173 (mp) REVERT: A 463 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.7590 (pp30) outliers start: 12 outliers final: 5 residues processed: 55 average time/residue: 1.3625 time to fit residues: 77.3886 Evaluate side-chains 54 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3999 Z= 0.155 Angle : 0.472 6.076 5426 Z= 0.238 Chirality : 0.038 0.156 616 Planarity : 0.004 0.031 674 Dihedral : 4.546 32.643 535 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.39 % Allowed : 21.05 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.40 (0.37), residues: 485 helix: 2.28 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.08 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.005 0.001 PHE A 509 TYR 0.011 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.457 Fit side-chains REVERT: A 16 LYS cc_start: 0.7400 (mtpp) cc_final: 0.7140 (pttp) REVERT: A 35 ARG cc_start: 0.7357 (mtt180) cc_final: 0.6745 (mpp-170) REVERT: A 115 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5587 (mp0) REVERT: A 219 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8415 (mmm160) REVERT: A 295 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8151 (mp) REVERT: A 396 GLN cc_start: 0.6786 (tt0) cc_final: 0.6568 (tt0) REVERT: A 463 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.7540 (pp30) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 1.4878 time to fit residues: 84.5006 Evaluate side-chains 55 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 45 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3999 Z= 0.155 Angle : 0.476 6.134 5426 Z= 0.240 Chirality : 0.038 0.157 616 Planarity : 0.004 0.031 674 Dihedral : 4.547 32.146 535 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.63 % Allowed : 21.05 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.40 (0.37), residues: 485 helix: 2.28 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.09 (0.49), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.006 0.001 PHE A 159 TYR 0.012 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.418 Fit side-chains REVERT: A 16 LYS cc_start: 0.7407 (mtpp) cc_final: 0.7149 (pttp) REVERT: A 35 ARG cc_start: 0.7334 (mtt180) cc_final: 0.6730 (mpp-170) REVERT: A 113 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7578 (mmt90) REVERT: A 115 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5568 (mp0) REVERT: A 219 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8416 (mmm160) REVERT: A 295 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8159 (mp) REVERT: A 463 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.7573 (pp30) outliers start: 11 outliers final: 5 residues processed: 57 average time/residue: 1.4413 time to fit residues: 84.8545 Evaluate side-chains 56 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 43 optimal weight: 0.0670 chunk 28 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 22 optimal weight: 0.0770 chunk 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.0270 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.2334 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3999 Z= 0.122 Angle : 0.433 5.405 5426 Z= 0.218 Chirality : 0.037 0.148 616 Planarity : 0.004 0.032 674 Dihedral : 4.233 30.069 535 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.91 % Allowed : 22.25 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.74 (0.38), residues: 485 helix: 2.55 (0.28), residues: 332 sheet: None (None), residues: 0 loop : 0.19 (0.50), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 131 HIS 0.002 0.001 HIS A 407 PHE 0.006 0.001 PHE A 159 TYR 0.009 0.001 TYR A 495 ARG 0.004 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.498 Fit side-chains REVERT: A 16 LYS cc_start: 0.7377 (mtpp) cc_final: 0.7154 (pttp) REVERT: A 35 ARG cc_start: 0.7114 (mtt180) cc_final: 0.6494 (mpp-170) REVERT: A 113 ARG cc_start: 0.7849 (mmm160) cc_final: 0.7596 (mmt90) REVERT: A 219 ARG cc_start: 0.8647 (OUTLIER) cc_final: 0.8412 (mmm160) REVERT: A 463 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.7459 (pp30) outliers start: 8 outliers final: 3 residues processed: 57 average time/residue: 1.4077 time to fit residues: 82.8927 Evaluate side-chains 52 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 ARG Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3999 Z= 0.199 Angle : 0.517 6.687 5426 Z= 0.259 Chirality : 0.039 0.161 616 Planarity : 0.004 0.030 674 Dihedral : 4.241 31.828 533 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.67 % Allowed : 22.73 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.36 (0.38), residues: 485 helix: 2.22 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.12 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 26 HIS 0.004 0.001 HIS A 312 PHE 0.008 0.001 PHE A 509 TYR 0.012 0.002 TYR A 495 ARG 0.006 0.000 ARG A 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.445 Fit side-chains REVERT: A 16 LYS cc_start: 0.7433 (mtpp) cc_final: 0.7222 (pttp) REVERT: A 35 ARG cc_start: 0.7349 (mtt180) cc_final: 0.6742 (mtm180) REVERT: A 113 ARG cc_start: 0.7885 (mmm160) cc_final: 0.7629 (mmt90) REVERT: A 463 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.7586 (pp30) outliers start: 7 outliers final: 3 residues processed: 52 average time/residue: 1.4441 time to fit residues: 77.5892 Evaluate side-chains 49 residues out of total 418 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TRP Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 504 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 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 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.116376 restraints weight = 4233.741| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.55 r_work: 0.3211 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3999 Z= 0.161 Angle : 0.487 6.192 5426 Z= 0.244 Chirality : 0.038 0.156 616 Planarity : 0.004 0.031 674 Dihedral : 4.146 27.949 533 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.20 % Allowed : 22.97 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 2.36 (0.38), residues: 485 helix: 2.24 (0.28), residues: 333 sheet: None (None), residues: 0 loop : 0.10 (0.50), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 247 HIS 0.003 0.001 HIS A 312 PHE 0.008 0.001 PHE A 159 TYR 0.011 0.001 TYR A 495 ARG 0.007 0.000 ARG A 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1919.67 seconds wall clock time: 35 minutes 6.28 seconds (2106.28 seconds total)