Starting phenix.real_space_refine on Fri Dec 27 05:39:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jt5_36633/12_2024/8jt5_36633.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jt5_36633/12_2024/8jt5_36633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jt5_36633/12_2024/8jt5_36633.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jt5_36633/12_2024/8jt5_36633.map" model { file = "/net/cci-nas-00/data/ceres_data/8jt5_36633/12_2024/8jt5_36633.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jt5_36633/12_2024/8jt5_36633.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.058 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 27 5.16 5 C 1901 2.51 5 N 444 2.21 5 O 482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 2854 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2846 Classifications: {'peptide': 384} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.98 Number of scatterers: 2854 At special positions: 0 Unit cell: (56.58, 62.32, 71.34, 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 27 16.00 O 482 8.00 N 444 7.00 C 1901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 381.4 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 692 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 92.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 52 removed outlier: 3.651A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Proline residue: A 42 - end of helix Proline residue: A 45 - end of helix removed outlier: 3.745A pdb=" N SER A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 157 removed outlier: 4.476A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.855A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 179 Processing helix chain 'A' and resid 181 through 211 Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.698A pdb=" N ILE A 223 " --> pdb=" O ASN A 219 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 270 removed outlier: 4.659A pdb=" N PHE A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 291 through 323 removed outlier: 3.753A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Proline residue: A 313 - end of helix Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 334 through 356 removed outlier: 4.894A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 Processing helix chain 'A' and resid 376 through 378 No H-bonds generated for 'chain 'A' and resid 376 through 378' Processing helix chain 'A' and resid 380 through 414 removed outlier: 4.638A pdb=" N ALA A 386 " --> pdb=" O TYR A 382 " (cutoff:3.500A) Proline residue: A 387 - end of helix Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 418 through 447 removed outlier: 3.666A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 435 " --> pdb=" O MET A 431 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 448 through 464 Processing helix chain 'A' and resid 465 through 471 removed outlier: 3.546A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 744 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.88 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 549 1.33 - 1.45: 652 1.45 - 1.57: 1675 1.57 - 1.69: 0 1.69 - 1.81: 46 Bond restraints: 2922 Sorted by residual: bond pdb=" CG HSM A 501 " pdb=" ND1 HSM A 501 " ideal model delta sigma weight residual 1.383 1.310 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" N ILE A 43 " pdb=" CA ILE A 43 " ideal model delta sigma weight residual 1.460 1.497 -0.038 1.21e-02 6.83e+03 9.61e+00 bond pdb=" N VAL A 26 " pdb=" CA VAL A 26 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.56e+00 bond pdb=" N ILE A 22 " pdb=" CA ILE A 22 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.19e-02 7.06e+03 8.38e+00 bond pdb=" CD2 HSM A 501 " pdb=" NE2 HSM A 501 " ideal model delta sigma weight residual 1.376 1.318 0.058 2.00e-02 2.50e+03 8.37e+00 ... (remaining 2917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 3823 1.94 - 3.89: 129 3.89 - 5.83: 20 5.83 - 7.77: 4 7.77 - 9.72: 2 Bond angle restraints: 3978 Sorted by residual: angle pdb=" CA VAL A 41 " pdb=" C VAL A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 120.83 123.43 -2.60 6.10e-01 2.69e+00 1.82e+01 angle pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta sigma weight residual 110.50 113.11 -2.61 6.30e-01 2.52e+00 1.72e+01 angle pdb=" CA VAL A 410 " pdb=" C VAL A 410 " pdb=" O VAL A 410 " ideal model delta sigma weight residual 120.95 117.29 3.66 1.04e+00 9.25e-01 1.24e+01 angle pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" O VAL A 40 " ideal model delta sigma weight residual 120.95 117.48 3.47 1.04e+00 9.25e-01 1.12e+01 angle pdb=" CA VAL A 41 " pdb=" C VAL A 41 " pdb=" O VAL A 41 " ideal model delta sigma weight residual 118.69 116.46 2.23 6.70e-01 2.23e+00 1.11e+01 ... (remaining 3973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 1502 17.36 - 34.73: 158 34.73 - 52.09: 41 52.09 - 69.46: 6 69.46 - 86.82: 2 Dihedral angle restraints: 1709 sinusoidal: 623 harmonic: 1086 Sorted by residual: dihedral pdb=" C ILE A 44 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual -122.00 -133.44 11.44 0 2.50e+00 1.60e-01 2.09e+01 dihedral pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CA ILE A 44 " pdb=" CB ILE A 44 " ideal model delta harmonic sigma weight residual 123.40 132.93 -9.53 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" CB GLU A 244 " pdb=" CG GLU A 244 " pdb=" CD GLU A 244 " pdb=" OE1 GLU A 244 " ideal model delta sinusoidal sigma weight residual 0.00 86.82 -86.82 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 1706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 378 0.054 - 0.108: 82 0.108 - 0.162: 14 0.162 - 0.216: 3 0.216 - 0.270: 2 Chirality restraints: 479 Sorted by residual: chirality pdb=" CA ILE A 44 " pdb=" N ILE A 44 " pdb=" C ILE A 44 " pdb=" CB ILE A 44 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA LEU A 23 " pdb=" N LEU A 23 " pdb=" C LEU A 23 " pdb=" CB LEU A 23 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CA VAL A 39 " pdb=" N VAL A 39 " pdb=" C VAL A 39 " pdb=" CB VAL A 39 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 7.84e-01 ... (remaining 476 not shown) Planarity restraints: 489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 166 " 0.003 2.00e-02 2.50e+03 1.74e-02 5.28e+00 pdb=" CG PHE A 166 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE A 166 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 166 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 PHE A 166 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 166 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 166 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 160 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO A 161 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 161 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 161 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 472 " -0.027 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 473 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " -0.023 5.00e-02 4.00e+02 ... (remaining 486 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 695 2.79 - 3.32: 2917 3.32 - 3.85: 4803 3.85 - 4.37: 5552 4.37 - 4.90: 9741 Nonbonded interactions: 23708 Sorted by model distance: nonbonded pdb=" O MET A 397 " pdb=" OG SER A 401 " model vdw 2.268 3.040 nonbonded pdb=" OD1 ASN A 305 " pdb=" ND1 HSM A 501 " model vdw 2.337 3.120 nonbonded pdb=" OD2 ASP A 33 " pdb=" OG SER A 196 " model vdw 2.400 3.040 nonbonded pdb=" N ASN A 128 " pdb=" OD1 ASN A 128 " model vdw 2.423 3.120 nonbonded pdb=" O LEU A 30 " pdb=" ND2 ASN A 34 " model vdw 2.458 3.120 ... (remaining 23703 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: 1.370 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.660 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.005 0.073 2922 Z= 0.332 Angle : 0.806 9.719 3978 Z= 0.489 Chirality : 0.050 0.270 479 Planarity : 0.006 0.052 489 Dihedral : 15.377 86.821 1017 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.11 % Favored : 97.63 % Rotamer: Outliers : 1.67 % Allowed : 23.67 % Favored : 74.67 % Cbeta Deviations : 0.29 % 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: 1.66 (0.42), residues: 380 helix: 1.63 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -1.89 (0.73), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.033 0.002 PHE A 166 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.500 Fit side-chains REVERT: A 40 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8588 (t) REVERT: A 47 TYR cc_start: 0.6836 (OUTLIER) cc_final: 0.6583 (t80) outliers start: 5 outliers final: 2 residues processed: 59 average time/residue: 0.1402 time to fit residues: 10.1228 Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 380 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 0.0670 chunk 22 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2922 Z= 0.263 Angle : 0.691 9.852 3978 Z= 0.334 Chirality : 0.042 0.152 479 Planarity : 0.006 0.055 489 Dihedral : 5.702 55.727 412 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.00 % Allowed : 25.33 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.43), residues: 380 helix: 1.77 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -1.65 (0.82), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.018 0.002 PHE A 238 TYR 0.017 0.001 TYR A 422 ARG 0.003 0.001 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.310 Fit side-chains REVERT: A 47 TYR cc_start: 0.6958 (OUTLIER) cc_final: 0.6525 (t80) outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.1188 time to fit residues: 8.4508 Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.0870 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.1980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.8204 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2922 Z= 0.218 Angle : 0.643 9.638 3978 Z= 0.309 Chirality : 0.041 0.152 479 Planarity : 0.006 0.055 489 Dihedral : 5.285 54.322 407 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.33 % Allowed : 24.00 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.43), residues: 380 helix: 1.79 (0.28), residues: 329 sheet: None (None), residues: 0 loop : -1.69 (0.86), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.002 0.001 HIS A 353 PHE 0.016 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.329 Fit side-chains REVERT: A 47 TYR cc_start: 0.6933 (OUTLIER) cc_final: 0.6495 (t80) outliers start: 7 outliers final: 3 residues processed: 61 average time/residue: 0.1518 time to fit residues: 11.2979 Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2922 Z= 0.261 Angle : 0.660 9.773 3978 Z= 0.317 Chirality : 0.042 0.140 479 Planarity : 0.006 0.055 489 Dihedral : 5.292 53.049 407 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.00 % Allowed : 21.33 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.43), residues: 380 helix: 1.75 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.61 (0.86), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.016 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.002 0.000 ARG A 471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.299 Fit side-chains REVERT: A 47 TYR cc_start: 0.6923 (OUTLIER) cc_final: 0.6478 (t80) REVERT: A 230 MET cc_start: 0.7499 (ttt) cc_final: 0.7272 (ttm) REVERT: A 433 TYR cc_start: 0.7718 (m-80) cc_final: 0.7384 (m-10) outliers start: 12 outliers final: 7 residues processed: 57 average time/residue: 0.1289 time to fit residues: 9.3805 Evaluate side-chains 52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8228 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2922 Z= 0.230 Angle : 0.644 9.613 3978 Z= 0.307 Chirality : 0.041 0.139 479 Planarity : 0.006 0.055 489 Dihedral : 5.216 51.799 407 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.00 % Allowed : 22.33 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.43), residues: 380 helix: 1.80 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.55 (0.86), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.002 0.001 HIS A 353 PHE 0.015 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.002 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.279 Fit side-chains REVERT: A 47 TYR cc_start: 0.6931 (OUTLIER) cc_final: 0.6467 (t80) REVERT: A 230 MET cc_start: 0.7509 (ttt) cc_final: 0.7292 (ttm) REVERT: A 433 TYR cc_start: 0.7677 (m-80) cc_final: 0.7460 (m-10) outliers start: 9 outliers final: 8 residues processed: 54 average time/residue: 0.1240 time to fit residues: 8.5053 Evaluate side-chains 54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 35 optimal weight: 0.0770 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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: 0.8227 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2922 Z= 0.226 Angle : 0.650 9.550 3978 Z= 0.309 Chirality : 0.041 0.131 479 Planarity : 0.006 0.055 489 Dihedral : 5.120 50.491 407 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.00 % Allowed : 21.67 % Favored : 74.33 % 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: 1.96 (0.44), residues: 380 helix: 1.76 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.72 (0.85), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.015 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.002 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.304 Fit side-chains REVERT: A 47 TYR cc_start: 0.6913 (OUTLIER) cc_final: 0.6449 (t80) REVERT: A 166 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.7325 (t80) REVERT: A 433 TYR cc_start: 0.7676 (m-80) cc_final: 0.7442 (m-10) outliers start: 12 outliers final: 9 residues processed: 57 average time/residue: 0.1208 time to fit residues: 8.7033 Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 47 TYR Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 23 optimal weight: 0.0270 chunk 24 optimal weight: 0.5980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 2922 Z= 0.221 Angle : 0.645 9.474 3978 Z= 0.307 Chirality : 0.041 0.135 479 Planarity : 0.006 0.058 489 Dihedral : 5.087 49.192 407 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.00 % Allowed : 23.00 % Favored : 74.00 % 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: 1.97 (0.44), residues: 380 helix: 1.76 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.71 (0.85), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 358 HIS 0.002 0.001 HIS A 353 PHE 0.014 0.001 PHE A 238 TYR 0.014 0.001 TYR A 422 ARG 0.001 0.000 ARG A 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.321 Fit side-chains REVERT: A 35 MET cc_start: 0.8288 (mtp) cc_final: 0.7942 (mtt) REVERT: A 166 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7303 (t80) REVERT: A 334 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7084 (m-80) REVERT: A 433 TYR cc_start: 0.7690 (m-80) cc_final: 0.7462 (m-10) outliers start: 9 outliers final: 7 residues processed: 55 average time/residue: 0.1353 time to fit residues: 9.3746 Evaluate side-chains 55 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0050 chunk 3 optimal weight: 0.9990 chunk 28 optimal weight: 0.0050 chunk 33 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.2980 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2922 Z= 0.189 Angle : 0.624 9.233 3978 Z= 0.295 Chirality : 0.040 0.134 479 Planarity : 0.006 0.058 489 Dihedral : 4.211 15.556 405 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 4.00 % Allowed : 22.00 % Favored : 74.00 % 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: 2.19 (0.44), residues: 380 helix: 1.89 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.62 (0.89), residues: 48 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 358 HIS 0.001 0.001 HIS A 353 PHE 0.013 0.001 PHE A 238 TYR 0.012 0.001 TYR A 422 ARG 0.001 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.314 Fit side-chains REVERT: A 166 PHE cc_start: 0.7492 (OUTLIER) cc_final: 0.7251 (t80) REVERT: A 334 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7000 (m-80) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.1365 time to fit residues: 10.3349 Evaluate side-chains 59 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 0.0070 chunk 37 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2922 Z= 0.245 Angle : 0.653 9.510 3978 Z= 0.311 Chirality : 0.042 0.133 479 Planarity : 0.006 0.060 489 Dihedral : 4.345 16.140 405 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 4.00 % Allowed : 22.00 % Favored : 74.00 % 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: 1.96 (0.44), residues: 380 helix: 1.76 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.70 (0.85), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 451 HIS 0.002 0.001 HIS A 353 PHE 0.014 0.001 PHE A 238 TYR 0.016 0.001 TYR A 422 ARG 0.004 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.316 Fit side-chains REVERT: A 35 MET cc_start: 0.8293 (mtp) cc_final: 0.7962 (mtt) REVERT: A 166 PHE cc_start: 0.7585 (OUTLIER) cc_final: 0.7308 (t80) REVERT: A 334 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7055 (m-80) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.1217 time to fit residues: 8.5451 Evaluate side-chains 57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 379 LYS Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 2922 Z= 0.340 Angle : 0.704 9.927 3978 Z= 0.339 Chirality : 0.044 0.145 479 Planarity : 0.006 0.057 489 Dihedral : 4.631 17.162 405 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.33 % Allowed : 22.33 % Favored : 74.33 % 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: 1.63 (0.43), residues: 380 helix: 1.48 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.46 (0.88), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.016 0.002 PHE A 238 TYR 0.019 0.001 TYR A 422 ARG 0.004 0.001 ARG A 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.312 Fit side-chains REVERT: A 35 MET cc_start: 0.8354 (mtp) cc_final: 0.8067 (mtt) REVERT: A 166 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7439 (t80) REVERT: A 334 PHE cc_start: 0.7818 (OUTLIER) cc_final: 0.7155 (m-80) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.1291 time to fit residues: 9.0085 Evaluate side-chains 56 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 169 MET Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 427 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.0270 chunk 1 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 0 optimal weight: 0.2980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.136437 restraints weight = 3340.869| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.72 r_work: 0.3398 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2922 Z= 0.232 Angle : 0.655 9.552 3978 Z= 0.314 Chirality : 0.042 0.134 479 Planarity : 0.006 0.057 489 Dihedral : 4.469 15.338 405 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.00 % Allowed : 23.00 % Favored : 74.00 % 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: 1.81 (0.43), residues: 380 helix: 1.64 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.63 (0.85), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 451 HIS 0.001 0.001 HIS A 353 PHE 0.014 0.001 PHE A 238 TYR 0.015 0.001 TYR A 422 ARG 0.004 0.001 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1091.65 seconds wall clock time: 20 minutes 31.53 seconds (1231.53 seconds total)