Starting phenix.real_space_refine on Fri Dec 27 09:26:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wx1_37897/12_2024/8wx1_37897.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wx1_37897/12_2024/8wx1_37897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wx1_37897/12_2024/8wx1_37897.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wx1_37897/12_2024/8wx1_37897.map" model { file = "/net/cci-nas-00/data/ceres_data/8wx1_37897/12_2024/8wx1_37897.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wx1_37897/12_2024/8wx1_37897.cif" } resolution = 3.64 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= 0.002 sd= 0.038 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 23 5.16 5 C 2593 2.51 5 N 640 2.21 5 O 670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 3926 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3926 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 25, 'TRANS': 474} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.98, per 1000 atoms: 0.76 Number of scatterers: 3926 At special positions: 0 Unit cell: (79.68, 74.1467, 69.72, 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 23 16.00 O 670 8.00 N 640 7.00 C 2593 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 533 " distance=2.03 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: 1.09 Conformation dependent library (CDL) restraints added in 542.0 milliseconds 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 926 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 79.6% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 25 through 61 removed outlier: 4.118A pdb=" N ASN A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL A 57 " --> pdb=" O THR A 53 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N LEU A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 97 Proline residue: A 88 - end of helix removed outlier: 4.076A pdb=" N TYR A 97 " --> pdb=" O LEU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 123 Processing helix chain 'A' and resid 123 through 131 removed outlier: 3.586A pdb=" N CYS A 131 " --> pdb=" O ARG A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 187 Processing helix chain 'A' and resid 191 through 224 Processing helix chain 'A' and resid 225 through 247 removed outlier: 3.884A pdb=" N GLY A 229 " --> pdb=" O SER A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 300 through 341 Proline residue: A 316 - end of helix Proline residue: A 323 - end of helix removed outlier: 3.641A pdb=" N HIS A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 399 removed outlier: 3.677A pdb=" N LEU A 383 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Proline residue: A 385 - end of helix Proline residue: A 393 - end of helix Processing helix chain 'A' and resid 403 through 435 removed outlier: 3.597A pdb=" N ALA A 435 " --> pdb=" O GLN A 431 " (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 457 through 483 removed outlier: 4.556A pdb=" N GLN A 461 " --> pdb=" O TRP A 457 " (cutoff:3.500A) Proline residue: A 475 - end of helix Processing helix chain 'A' and resid 488 through 515 Processing helix chain 'A' and resid 535 through 566 Processing sheet with id=AA1, first strand: chain 'A' and resid 439 through 443 removed outlier: 3.961A pdb=" N ILE A 443 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 446 " --> pdb=" O ILE A 443 " (cutoff:3.500A) 314 hydrogen bonds defined for protein. 939 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: 1.11 Time building geometry restraints manager: 1.26 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: 1194 1.34 - 1.46: 919 1.46 - 1.58: 1879 1.58 - 1.70: 0 1.70 - 1.81: 37 Bond restraints: 4029 Sorted by residual: bond pdb=" C SER A 154 " pdb=" N PRO A 155 " ideal model delta sigma weight residual 1.331 1.362 -0.031 1.27e-02 6.20e+03 5.85e+00 bond pdb=" C VAL A 322 " pdb=" N PRO A 323 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.77e+00 bond pdb=" C ILE A 474 " pdb=" N PRO A 475 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.19e+00 bond pdb=" C ALA A 87 " pdb=" N PRO A 88 " ideal model delta sigma weight residual 1.336 1.357 -0.021 1.20e-02 6.94e+03 3.12e+00 bond pdb=" C LEU A 315 " pdb=" N PRO A 316 " ideal model delta sigma weight residual 1.335 1.356 -0.022 1.28e-02 6.10e+03 2.87e+00 ... (remaining 4024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 5103 1.29 - 2.59: 298 2.59 - 3.88: 59 3.88 - 5.17: 20 5.17 - 6.47: 7 Bond angle restraints: 5487 Sorted by residual: angle pdb=" N VAL A 187 " pdb=" CA VAL A 187 " pdb=" C VAL A 187 " ideal model delta sigma weight residual 111.91 108.05 3.86 8.90e-01 1.26e+00 1.88e+01 angle pdb=" C GLN A 458 " pdb=" N ILE A 459 " pdb=" CA ILE A 459 " ideal model delta sigma weight residual 120.33 123.30 -2.97 8.00e-01 1.56e+00 1.38e+01 angle pdb=" C VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 113.70 110.40 3.30 9.50e-01 1.11e+00 1.21e+01 angle pdb=" C TRP A 152 " pdb=" N SER A 153 " pdb=" CA SER A 153 " ideal model delta sigma weight residual 122.74 127.50 -4.76 1.44e+00 4.82e-01 1.09e+01 angle pdb=" CA ARG A 366 " pdb=" C ARG A 366 " pdb=" N ILE A 367 " ideal model delta sigma weight residual 114.17 118.88 -4.71 1.45e+00 4.76e-01 1.05e+01 ... (remaining 5482 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.16: 2100 17.16 - 34.33: 207 34.33 - 51.49: 31 51.49 - 68.66: 6 68.66 - 85.82: 4 Dihedral angle restraints: 2348 sinusoidal: 906 harmonic: 1442 Sorted by residual: dihedral pdb=" CA MET A 188 " pdb=" C MET A 188 " pdb=" N ASP A 189 " pdb=" CA ASP A 189 " ideal model delta harmonic sigma weight residual -180.00 -147.74 -32.26 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA CYS A 273 " pdb=" C CYS A 273 " pdb=" N PRO A 274 " pdb=" CA PRO A 274 " ideal model delta harmonic sigma weight residual 180.00 163.53 16.47 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA ASN A 346 " pdb=" CB ASN A 346 " pdb=" CG ASN A 346 " pdb=" OD1 ASN A 346 " ideal model delta sinusoidal sigma weight residual 120.00 -174.37 -65.63 2 2.00e+01 2.50e-03 9.96e+00 ... (remaining 2345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 436 0.027 - 0.054: 100 0.054 - 0.081: 68 0.081 - 0.109: 20 0.109 - 0.136: 5 Chirality restraints: 629 Sorted by residual: chirality pdb=" CA ILE A 224 " pdb=" N ILE A 224 " pdb=" C ILE A 224 " pdb=" CB ILE A 224 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 chirality pdb=" CA ILE A 344 " pdb=" N ILE A 344 " pdb=" C ILE A 344 " pdb=" CB ILE A 344 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA PRO A 368 " pdb=" N PRO A 368 " pdb=" C PRO A 368 " pdb=" CB PRO A 368 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 626 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 26 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 27 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 27 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 27 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 214 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C LEU A 214 " 0.026 2.00e-02 2.50e+03 pdb=" O LEU A 214 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 215 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 439 " -0.024 5.00e-02 4.00e+02 3.60e-02 2.07e+00 pdb=" N PRO A 440 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 440 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 440 " -0.020 5.00e-02 4.00e+02 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1147 2.82 - 3.34: 4189 3.34 - 3.86: 6800 3.86 - 4.38: 7128 4.38 - 4.90: 12352 Nonbonded interactions: 31616 Sorted by model distance: nonbonded pdb=" O ARG A 29 " pdb=" OG1 THR A 33 " model vdw 2.297 3.040 nonbonded pdb=" O SER A 259 " pdb=" OG SER A 259 " model vdw 2.300 3.040 nonbonded pdb=" O ASP A 526 " pdb=" ND2 ASN A 529 " model vdw 2.384 3.120 nonbonded pdb=" O PRO A 402 " pdb=" NZ LYS A 407 " model vdw 2.390 3.120 nonbonded pdb=" O MET A 188 " pdb=" N LEU A 190 " model vdw 2.400 3.120 ... (remaining 31611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.980 Find NCS groups from input model: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 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 : 0.003 0.031 4029 Z= 0.171 Angle : 0.737 6.466 5487 Z= 0.464 Chirality : 0.035 0.136 629 Planarity : 0.004 0.041 680 Dihedral : 13.802 85.821 1416 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.67 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: 0.07 (0.37), residues: 492 helix: 0.75 (0.24), residues: 386 sheet: None (None), residues: 0 loop : -2.47 (0.69), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 30 HIS 0.001 0.000 HIS A 341 PHE 0.010 0.001 PHE A 479 TYR 0.012 0.001 TYR A 324 ARG 0.003 0.000 ARG A 196 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.7149 (tm-30) cc_final: 0.6772 (tm-30) REVERT: A 474 ILE cc_start: 0.8674 (mm) cc_final: 0.8357 (mm) REVERT: A 552 LEU cc_start: 0.8554 (tp) cc_final: 0.8319 (tt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1469 time to fit residues: 28.3186 Evaluate side-chains 109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 0.0270 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 45 optimal weight: 0.0050 overall best weight: 0.5652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 565 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4029 Z= 0.196 Angle : 0.668 10.130 5487 Z= 0.327 Chirality : 0.039 0.178 629 Planarity : 0.005 0.038 680 Dihedral : 4.336 26.714 540 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.08 % Favored : 94.51 % Rotamer: Outliers : 2.15 % Allowed : 18.42 % Favored : 79.43 % 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: 1.56 (0.40), residues: 492 helix: 1.78 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.75 (0.71), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 30 HIS 0.002 0.001 HIS A 341 PHE 0.024 0.001 PHE A 496 TYR 0.021 0.002 TYR A 481 ARG 0.004 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 112 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ASN cc_start: 0.7573 (p0) cc_final: 0.7367 (p0) REVERT: A 188 MET cc_start: 0.7795 (tpp) cc_final: 0.6980 (ttt) REVERT: A 335 TYR cc_start: 0.8547 (m-10) cc_final: 0.8213 (m-10) REVERT: A 552 LEU cc_start: 0.8608 (tp) cc_final: 0.8315 (tt) outliers start: 9 outliers final: 7 residues processed: 116 average time/residue: 0.1189 time to fit residues: 17.9810 Evaluate side-chains 111 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 TRP Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 344 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 0.0570 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.0870 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 330 GLN ** A 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4029 Z= 0.186 Angle : 0.629 9.531 5487 Z= 0.309 Chirality : 0.040 0.199 629 Planarity : 0.005 0.039 680 Dihedral : 4.247 24.873 540 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.49 % Favored : 94.11 % Rotamer: Outliers : 2.87 % Allowed : 20.33 % Favored : 76.79 % 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: 1.89 (0.40), residues: 492 helix: 1.98 (0.26), residues: 386 sheet: None (None), residues: 0 loop : -1.55 (0.73), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 30 HIS 0.001 0.000 HIS A 341 PHE 0.020 0.001 PHE A 496 TYR 0.012 0.001 TYR A 324 ARG 0.004 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 108 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 328 TYR cc_start: 0.8909 (t80) cc_final: 0.8334 (t80) REVERT: A 335 TYR cc_start: 0.8608 (m-10) cc_final: 0.8133 (m-10) REVERT: A 552 LEU cc_start: 0.8532 (tp) cc_final: 0.8296 (tt) outliers start: 12 outliers final: 9 residues processed: 111 average time/residue: 0.1132 time to fit residues: 16.6530 Evaluate side-chains 106 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 TRP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 428 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.0270 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN A 461 GLN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4029 Z= 0.185 Angle : 0.616 8.306 5487 Z= 0.306 Chirality : 0.040 0.170 629 Planarity : 0.005 0.036 680 Dihedral : 4.274 25.152 540 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.10 % Favored : 93.50 % Rotamer: Outliers : 3.11 % Allowed : 23.21 % Favored : 73.68 % 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: 2.16 (0.41), residues: 492 helix: 2.11 (0.26), residues: 384 sheet: None (None), residues: 0 loop : -1.11 (0.76), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 30 HIS 0.001 0.000 HIS A 341 PHE 0.023 0.001 PHE A 527 TYR 0.015 0.001 TYR A 560 ARG 0.004 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8520 (tp) cc_final: 0.8262 (tp) REVERT: A 328 TYR cc_start: 0.8890 (t80) cc_final: 0.8356 (t80) REVERT: A 335 TYR cc_start: 0.8607 (m-10) cc_final: 0.8238 (m-10) REVERT: A 552 LEU cc_start: 0.8523 (tp) cc_final: 0.8287 (tt) outliers start: 13 outliers final: 9 residues processed: 105 average time/residue: 0.1232 time to fit residues: 17.4999 Evaluate side-chains 111 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 92 TRP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 428 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4029 Z= 0.212 Angle : 0.624 7.595 5487 Z= 0.313 Chirality : 0.040 0.158 629 Planarity : 0.005 0.040 680 Dihedral : 4.212 20.806 540 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.89 % Favored : 93.70 % Rotamer: Outliers : 4.31 % Allowed : 23.44 % Favored : 72.25 % 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: 2.29 (0.41), residues: 492 helix: 2.20 (0.26), residues: 384 sheet: -1.86 (1.57), residues: 10 loop : -0.93 (0.82), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 30 HIS 0.001 0.000 HIS A 343 PHE 0.030 0.002 PHE A 527 TYR 0.011 0.001 TYR A 324 ARG 0.004 0.000 ARG A 127 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 98 LEU cc_start: 0.8613 (tp) cc_final: 0.8365 (tp) REVERT: A 328 TYR cc_start: 0.8954 (t80) cc_final: 0.8507 (t80) REVERT: A 335 TYR cc_start: 0.8626 (m-10) cc_final: 0.8344 (m-10) REVERT: A 481 TYR cc_start: 0.8874 (t80) cc_final: 0.8620 (t80) REVERT: A 527 PHE cc_start: 0.4928 (p90) cc_final: 0.4713 (p90) REVERT: A 561 GLU cc_start: 0.8485 (tp30) cc_final: 0.8062 (tm-30) outliers start: 18 outliers final: 11 residues processed: 107 average time/residue: 0.1128 time to fit residues: 16.1446 Evaluate side-chains 108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 92 TRP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 459 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 9.9990 chunk 48 optimal weight: 0.7980 chunk 40 optimal weight: 0.0970 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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: 0.7386 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4029 Z= 0.185 Angle : 0.631 12.443 5487 Z= 0.313 Chirality : 0.040 0.158 629 Planarity : 0.005 0.040 680 Dihedral : 4.211 20.513 540 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.89 % Favored : 93.70 % Rotamer: Outliers : 3.83 % Allowed : 23.44 % Favored : 72.73 % 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: 2.36 (0.41), residues: 492 helix: 2.23 (0.26), residues: 383 sheet: -1.42 (1.88), residues: 10 loop : -0.81 (0.84), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 30 HIS 0.001 0.000 HIS A 343 PHE 0.021 0.001 PHE A 527 TYR 0.011 0.001 TYR A 560 ARG 0.007 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 328 TYR cc_start: 0.8917 (t80) cc_final: 0.8423 (t80) REVERT: A 335 TYR cc_start: 0.8586 (m-10) cc_final: 0.8341 (m-10) REVERT: A 481 TYR cc_start: 0.8838 (t80) cc_final: 0.8539 (t80) REVERT: A 527 PHE cc_start: 0.5080 (p90) cc_final: 0.4865 (p90) REVERT: A 552 LEU cc_start: 0.8592 (tp) cc_final: 0.8360 (tt) REVERT: A 561 GLU cc_start: 0.8462 (tp30) cc_final: 0.8070 (tm-30) outliers start: 16 outliers final: 12 residues processed: 108 average time/residue: 0.1218 time to fit residues: 17.1256 Evaluate side-chains 108 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 92 TRP Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 506 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 0.5980 chunk 40 optimal weight: 0.2980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4029 Z= 0.208 Angle : 0.652 10.222 5487 Z= 0.321 Chirality : 0.041 0.261 629 Planarity : 0.006 0.102 680 Dihedral : 4.274 19.348 540 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.30 % Favored : 93.29 % Rotamer: Outliers : 3.83 % Allowed : 24.64 % Favored : 71.53 % 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: 2.33 (0.41), residues: 492 helix: 2.23 (0.26), residues: 383 sheet: -1.39 (1.95), residues: 10 loop : -0.95 (0.81), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 30 HIS 0.001 0.000 HIS A 343 PHE 0.019 0.001 PHE A 527 TYR 0.010 0.001 TYR A 156 ARG 0.007 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 328 TYR cc_start: 0.8945 (t80) cc_final: 0.8467 (t80) REVERT: A 335 TYR cc_start: 0.8584 (m-10) cc_final: 0.8275 (m-10) REVERT: A 454 SER cc_start: 0.7652 (m) cc_final: 0.7299 (t) REVERT: A 481 TYR cc_start: 0.8828 (t80) cc_final: 0.8536 (t80) REVERT: A 489 GLN cc_start: 0.6963 (OUTLIER) cc_final: 0.6560 (mt0) REVERT: A 552 LEU cc_start: 0.8608 (tp) cc_final: 0.8377 (tt) REVERT: A 561 GLU cc_start: 0.8454 (tp30) cc_final: 0.8067 (tm-30) outliers start: 16 outliers final: 10 residues processed: 105 average time/residue: 0.1074 time to fit residues: 15.1834 Evaluate side-chains 109 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain A residue 506 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 10.0000 chunk 4 optimal weight: 0.2980 chunk 37 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 46 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4029 Z= 0.199 Angle : 0.653 9.679 5487 Z= 0.322 Chirality : 0.041 0.195 629 Planarity : 0.005 0.071 680 Dihedral : 4.272 18.917 540 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.10 % Favored : 93.50 % Rotamer: Outliers : 4.07 % Allowed : 24.88 % Favored : 71.05 % 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: 2.34 (0.41), residues: 492 helix: 2.23 (0.26), residues: 383 sheet: -1.30 (1.98), residues: 10 loop : -0.91 (0.81), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 30 HIS 0.001 0.000 HIS A 343 PHE 0.016 0.001 PHE A 496 TYR 0.012 0.001 TYR A 156 ARG 0.006 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.438 Fit side-chains revert: symmetry clash REVERT: A 125 ASP cc_start: 0.7884 (m-30) cc_final: 0.7497 (t0) REVERT: A 328 TYR cc_start: 0.8944 (t80) cc_final: 0.8444 (t80) REVERT: A 335 TYR cc_start: 0.8575 (m-10) cc_final: 0.8323 (m-10) REVERT: A 454 SER cc_start: 0.7731 (m) cc_final: 0.7386 (t) REVERT: A 481 TYR cc_start: 0.8788 (t80) cc_final: 0.8530 (t80) REVERT: A 489 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6550 (mt0) REVERT: A 561 GLU cc_start: 0.8478 (tp30) cc_final: 0.8091 (tm-30) outliers start: 17 outliers final: 14 residues processed: 113 average time/residue: 0.1077 time to fit residues: 16.4779 Evaluate side-chains 118 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 275 CYS Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 489 GLN Chi-restraints excluded: chain A residue 506 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4029 Z= 0.206 Angle : 0.664 9.185 5487 Z= 0.328 Chirality : 0.042 0.191 629 Planarity : 0.005 0.059 680 Dihedral : 4.272 18.945 540 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.30 % Favored : 93.29 % Rotamer: Outliers : 3.59 % Allowed : 26.56 % Favored : 69.86 % 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: 2.32 (0.41), residues: 492 helix: 2.21 (0.26), residues: 383 sheet: -1.37 (1.95), residues: 10 loop : -0.88 (0.81), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 30 HIS 0.001 0.000 HIS A 343 PHE 0.017 0.001 PHE A 496 TYR 0.010 0.001 TYR A 324 ARG 0.005 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 125 ASP cc_start: 0.7887 (m-30) cc_final: 0.7496 (t0) REVERT: A 335 TYR cc_start: 0.8611 (m-10) cc_final: 0.8331 (m-10) REVERT: A 454 SER cc_start: 0.7666 (m) cc_final: 0.7412 (t) REVERT: A 481 TYR cc_start: 0.8791 (t80) cc_final: 0.8502 (t80) REVERT: A 489 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6641 (mt0) REVERT: A 561 GLU cc_start: 0.8457 (tp30) cc_final: 0.8068 (tm-30) outliers start: 15 outliers final: 10 residues processed: 111 average time/residue: 0.1142 time to fit residues: 17.1107 Evaluate side-chains 114 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 489 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 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 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4029 Z= 0.210 Angle : 0.668 11.123 5487 Z= 0.333 Chirality : 0.042 0.184 629 Planarity : 0.005 0.060 680 Dihedral : 4.282 20.059 540 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.69 % Favored : 93.90 % Rotamer: Outliers : 3.59 % Allowed : 27.03 % Favored : 69.38 % 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: 2.39 (0.41), residues: 492 helix: 2.23 (0.26), residues: 383 sheet: -1.22 (1.97), residues: 10 loop : -0.74 (0.81), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 92 HIS 0.001 0.000 HIS A 343 PHE 0.016 0.001 PHE A 496 TYR 0.010 0.001 TYR A 324 ARG 0.005 0.000 ARG A 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 984 Ramachandran restraints generated. 492 Oldfield, 0 Emsley, 492 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 105 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 125 ASP cc_start: 0.7893 (m-30) cc_final: 0.7508 (t0) REVERT: A 161 LEU cc_start: 0.8659 (mt) cc_final: 0.8403 (mt) REVERT: A 303 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7754 (tm-30) REVERT: A 328 TYR cc_start: 0.8998 (t80) cc_final: 0.8517 (t80) REVERT: A 335 TYR cc_start: 0.8657 (m-10) cc_final: 0.8268 (m-10) REVERT: A 454 SER cc_start: 0.7696 (m) cc_final: 0.7451 (t) REVERT: A 481 TYR cc_start: 0.8785 (t80) cc_final: 0.8501 (t80) REVERT: A 489 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6755 (mt0) REVERT: A 561 GLU cc_start: 0.8421 (tp30) cc_final: 0.8038 (tm-30) outliers start: 15 outliers final: 12 residues processed: 112 average time/residue: 0.1235 time to fit residues: 18.2197 Evaluate side-chains 117 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 243 ILE Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 420 ILE Chi-restraints excluded: chain A residue 428 GLU Chi-restraints excluded: chain A residue 459 ILE Chi-restraints excluded: chain A residue 489 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 30 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.171130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143456 restraints weight = 5412.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147596 restraints weight = 2907.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.150322 restraints weight = 1987.510| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.4083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4029 Z= 0.199 Angle : 0.658 9.097 5487 Z= 0.327 Chirality : 0.041 0.182 629 Planarity : 0.006 0.073 680 Dihedral : 4.277 18.192 540 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.30 % Favored : 93.50 % Rotamer: Outliers : 3.11 % Allowed : 27.75 % Favored : 69.14 % 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: 2.42 (0.41), residues: 492 helix: 2.24 (0.26), residues: 383 sheet: None (None), residues: 0 loop : -0.76 (0.76), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 30 HIS 0.001 0.000 HIS A 341 PHE 0.016 0.001 PHE A 496 TYR 0.010 0.001 TYR A 324 ARG 0.013 0.001 ARG A 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1191.83 seconds wall clock time: 22 minutes 56.18 seconds (1376.18 seconds total)