Starting phenix.real_space_refine on Fri Dec 27 11:41:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnc_34910/12_2024/8hnc_34910.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnc_34910/12_2024/8hnc_34910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnc_34910/12_2024/8hnc_34910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnc_34910/12_2024/8hnc_34910.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnc_34910/12_2024/8hnc_34910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnc_34910/12_2024/8hnc_34910.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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 33 5.16 5 C 2825 2.51 5 N 678 2.21 5 O 736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 4272 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4187 Classifications: {'peptide': 570} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 21, 'TRANS': 548} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 5, 'ASN:plan1': 10, 'ASP:plan': 5, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 132 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'BLR': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.51, per 1000 atoms: 0.82 Number of scatterers: 4272 At special positions: 0 Unit cell: (101.504, 59.904, 79.872, 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 33 16.00 O 736 8.00 N 678 7.00 C 2825 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.04 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.01 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 704 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 600.6 milliseconds 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1036 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 1 sheets defined 66.1% alpha, 0.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 26 through 49 removed outlier: 4.087A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 58 Processing helix chain 'A' and resid 62 through 79 removed outlier: 4.505A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.946A pdb=" N PHE A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 121 through 125 removed outlier: 4.652A pdb=" N LYS A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 165 Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.085A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 200 removed outlier: 3.844A pdb=" N SER A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 216 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 258 through 274 removed outlier: 3.594A pdb=" N PHE A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.815A pdb=" N LEU A 279 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 Processing helix chain 'A' and resid 335 through 366 removed outlier: 5.253A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 400 removed outlier: 3.757A pdb=" N GLY A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 426 removed outlier: 3.767A pdb=" N PHE A 426 " --> pdb=" O TYR A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.827A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR A 535 " --> pdb=" O THR A 531 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 563 removed outlier: 3.537A pdb=" N VAL A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 567 through 584 Processing helix chain 'A' and resid 586 through 597 Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 481 263 hydrogen bonds defined for protein. 777 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: 1.16 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 664 1.32 - 1.45: 1233 1.45 - 1.57: 2432 1.57 - 1.69: 0 1.69 - 1.82: 49 Bond restraints: 4378 Sorted by residual: bond pdb=" CGD BLR A 701 " pdb=" O1D BLR A 701 " ideal model delta sigma weight residual 1.231 1.308 -0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" N LEU A 545 " pdb=" CA LEU A 545 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.28e-02 6.10e+03 1.31e+01 bond pdb=" C TYR A 352 " pdb=" O TYR A 352 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" CA LEU A 545 " pdb=" C LEU A 545 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.35e-02 5.49e+03 9.96e+00 bond pdb=" CA TYR A 352 " pdb=" C TYR A 352 " ideal model delta sigma weight residual 1.524 1.483 0.041 1.32e-02 5.74e+03 9.53e+00 ... (remaining 4373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 5701 2.22 - 4.44: 206 4.44 - 6.66: 32 6.66 - 8.88: 9 8.88 - 11.10: 3 Bond angle restraints: 5951 Sorted by residual: angle pdb=" N VAL A 509 " pdb=" CA VAL A 509 " pdb=" C VAL A 509 " ideal model delta sigma weight residual 110.62 118.68 -8.06 1.02e+00 9.61e-01 6.25e+01 angle pdb=" N ASN A 503 " pdb=" CA ASN A 503 " pdb=" C ASN A 503 " ideal model delta sigma weight residual 111.56 122.66 -11.10 1.43e+00 4.89e-01 6.02e+01 angle pdb=" C THR A 186 " pdb=" N PRO A 187 " pdb=" CA PRO A 187 " ideal model delta sigma weight residual 121.65 115.05 6.60 1.01e+00 9.80e-01 4.27e+01 angle pdb=" C TRP A 254 " pdb=" N VAL A 255 " pdb=" CA VAL A 255 " ideal model delta sigma weight residual 122.99 114.19 8.80 1.39e+00 5.18e-01 4.01e+01 angle pdb=" C THR A 510 " pdb=" N GLY A 511 " pdb=" CA GLY A 511 " ideal model delta sigma weight residual 121.58 116.85 4.73 8.60e-01 1.35e+00 3.02e+01 ... (remaining 5946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.20: 2389 21.20 - 42.40: 142 42.40 - 63.60: 13 63.60 - 84.79: 11 84.79 - 105.99: 8 Dihedral angle restraints: 2563 sinusoidal: 936 harmonic: 1627 Sorted by residual: dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 506 " pdb=" CB CYS A 506 " ideal model delta sinusoidal sigma weight residual 93.00 175.59 -82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 463 " pdb=" CB CYS A 463 " ideal model delta sinusoidal sigma weight residual 93.00 14.62 78.38 1 1.00e+01 1.00e-02 7.67e+01 dihedral pdb=" C LEU A 143 " pdb=" N LEU A 143 " pdb=" CA LEU A 143 " pdb=" CB LEU A 143 " ideal model delta harmonic sigma weight residual -122.60 -110.31 -12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 2560 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 691 0.294 - 0.587: 3 0.587 - 0.881: 0 0.881 - 1.175: 0 1.175 - 1.468: 1 Chirality restraints: 695 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-02 2.50e+03 5.39e+03 chirality pdb=" CA ASN A 503 " pdb=" N ASN A 503 " pdb=" C ASN A 503 " pdb=" CB ASN A 503 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA ASN A 460 " pdb=" N ASN A 460 " pdb=" C ASN A 460 " pdb=" CB ASN A 460 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 692 not shown) Planarity restraints: 728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.313 2.00e-02 2.50e+03 2.66e-01 8.82e+02 pdb=" C7 NAG B 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " 0.286 2.00e-02 2.50e+03 2.44e-01 7.46e+02 pdb=" C7 NAG B 1 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.018 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " -0.412 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 704 " -0.159 2.00e-02 2.50e+03 1.31e-01 2.14e+02 pdb=" C7 NAG A 704 " 0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 704 " -0.118 2.00e-02 2.50e+03 pdb=" N2 NAG A 704 " 0.210 2.00e-02 2.50e+03 pdb=" O7 NAG A 704 " 0.022 2.00e-02 2.50e+03 ... (remaining 725 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 53 2.64 - 3.21: 4287 3.21 - 3.77: 6608 3.77 - 4.34: 8538 4.34 - 4.90: 13867 Nonbonded interactions: 33353 Sorted by model distance: nonbonded pdb=" ND BLR A 701 " pdb=" O2A BLR A 701 " model vdw 2.079 3.120 nonbonded pdb=" O MET A 233 " pdb=" N ALA A 257 " model vdw 2.204 3.120 nonbonded pdb=" O ASN A 460 " pdb=" N CYS A 463 " model vdw 2.224 3.120 nonbonded pdb=" OG SER A 418 " pdb=" ND2 ASN A 544 " model vdw 2.293 3.120 nonbonded pdb=" ND1 HIS A 115 " pdb=" CD1 TRP A 259 " model vdw 2.364 3.340 ... (remaining 33348 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.970 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.210 Find NCS groups from input model: 0.040 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 4378 Z= 0.403 Angle : 1.009 11.099 5951 Z= 0.640 Chirality : 0.081 1.468 695 Planarity : 0.015 0.266 726 Dihedral : 15.074 105.991 1506 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.49 % Allowed : 5.11 % Favored : 94.40 % Cbeta Deviations : 0.39 % 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: -2.79 (0.31), residues: 562 helix: -1.27 (0.24), residues: 343 sheet: None (None), residues: 0 loop : -2.72 (0.37), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 258 HIS 0.002 0.001 HIS A 92 PHE 0.029 0.001 PHE A 591 TYR 0.025 0.002 TYR A 352 ARG 0.001 0.000 ARG A 57 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8898 (tpt) cc_final: 0.8483 (tpp) REVERT: A 185 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8113 (tm-30) REVERT: A 381 ILE cc_start: 0.8682 (tp) cc_final: 0.8426 (tp) REVERT: A 617 ASN cc_start: 0.7996 (t0) cc_final: 0.7607 (t0) outliers start: 2 outliers final: 0 residues processed: 106 average time/residue: 0.2003 time to fit residues: 25.9884 Evaluate side-chains 75 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 48 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 544 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4378 Z= 0.227 Angle : 0.652 8.853 5951 Z= 0.316 Chirality : 0.043 0.265 695 Planarity : 0.004 0.039 726 Dihedral : 8.761 85.736 680 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.46 % Allowed : 14.11 % Favored : 84.43 % 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: -0.48 (0.34), residues: 562 helix: 0.59 (0.28), residues: 346 sheet: None (None), residues: 0 loop : -1.81 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.003 0.001 HIS A 92 PHE 0.013 0.001 PHE A 591 TYR 0.029 0.002 TYR A 590 ARG 0.005 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8959 (tpt) cc_final: 0.8523 (tpp) REVERT: A 381 ILE cc_start: 0.8718 (tp) cc_final: 0.8423 (tp) REVERT: A 390 MET cc_start: 0.8343 (mmt) cc_final: 0.7763 (mmt) outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 0.1538 time to fit residues: 16.9623 Evaluate side-chains 80 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 50.0000 chunk 35 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 41 optimal weight: 0.0470 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4378 Z= 0.205 Angle : 0.589 7.713 5951 Z= 0.287 Chirality : 0.042 0.272 695 Planarity : 0.004 0.040 726 Dihedral : 7.486 83.087 680 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.16 % Allowed : 16.55 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.36), residues: 562 helix: 1.28 (0.28), residues: 340 sheet: None (None), residues: 0 loop : -1.44 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.002 0.001 HIS A 92 PHE 0.013 0.001 PHE A 591 TYR 0.024 0.002 TYR A 590 ARG 0.006 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8901 (tpt) cc_final: 0.8500 (tpp) REVERT: A 170 MET cc_start: 0.7862 (mmm) cc_final: 0.7618 (mmm) REVERT: A 198 ASP cc_start: 0.8705 (t0) cc_final: 0.8439 (t0) REVERT: A 381 ILE cc_start: 0.8730 (tp) cc_final: 0.8436 (tp) REVERT: A 390 MET cc_start: 0.8214 (mmt) cc_final: 0.7606 (mmt) REVERT: A 600 ILE cc_start: 0.9054 (tp) cc_final: 0.8741 (tp) REVERT: A 615 THR cc_start: 0.7602 (OUTLIER) cc_final: 0.7390 (p) outliers start: 13 outliers final: 7 residues processed: 88 average time/residue: 0.1370 time to fit residues: 15.9772 Evaluate side-chains 83 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 615 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 5 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4378 Z= 0.215 Angle : 0.575 6.579 5951 Z= 0.283 Chirality : 0.042 0.204 695 Planarity : 0.004 0.051 726 Dihedral : 7.140 80.487 680 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.41 % Allowed : 18.00 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.36), residues: 562 helix: 1.48 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -1.47 (0.40), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 92 PHE 0.013 0.001 PHE A 591 TYR 0.025 0.002 TYR A 590 ARG 0.006 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8906 (tpt) cc_final: 0.8495 (tpp) REVERT: A 381 ILE cc_start: 0.8764 (tp) cc_final: 0.8453 (tp) REVERT: A 390 MET cc_start: 0.8198 (mmt) cc_final: 0.7483 (mmt) outliers start: 14 outliers final: 8 residues processed: 89 average time/residue: 0.1587 time to fit residues: 18.8825 Evaluate side-chains 85 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 2.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 41 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 10 optimal weight: 30.0000 chunk 32 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 365 GLN A 520 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4378 Z= 0.210 Angle : 0.567 6.315 5951 Z= 0.281 Chirality : 0.041 0.207 695 Planarity : 0.004 0.040 726 Dihedral : 6.948 78.378 680 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.14 % Allowed : 18.25 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.36), residues: 562 helix: 1.58 (0.28), residues: 347 sheet: None (None), residues: 0 loop : -1.20 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.005 0.001 HIS A 92 PHE 0.011 0.001 PHE A 591 TYR 0.023 0.002 TYR A 590 ARG 0.007 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8892 (tpt) cc_final: 0.8493 (tpp) REVERT: A 176 MET cc_start: 0.8157 (tpp) cc_final: 0.7888 (mmt) REVERT: A 381 ILE cc_start: 0.8777 (tp) cc_final: 0.8466 (tp) REVERT: A 390 MET cc_start: 0.8173 (mmt) cc_final: 0.7449 (mmt) outliers start: 17 outliers final: 8 residues processed: 89 average time/residue: 0.1384 time to fit residues: 16.5458 Evaluate side-chains 83 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 13 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 25 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4378 Z= 0.188 Angle : 0.581 7.219 5951 Z= 0.284 Chirality : 0.041 0.194 695 Planarity : 0.004 0.035 726 Dihedral : 6.787 75.006 680 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.65 % Allowed : 19.22 % Favored : 77.13 % 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: 1.02 (0.37), residues: 562 helix: 1.76 (0.29), residues: 347 sheet: None (None), residues: 0 loop : -1.17 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 92 PHE 0.010 0.001 PHE A 116 TYR 0.023 0.001 TYR A 590 ARG 0.005 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8861 (tpt) cc_final: 0.8502 (tpp) REVERT: A 170 MET cc_start: 0.7511 (mmm) cc_final: 0.7233 (mmm) REVERT: A 381 ILE cc_start: 0.8747 (tp) cc_final: 0.8430 (tp) REVERT: A 390 MET cc_start: 0.8121 (mmt) cc_final: 0.7391 (mmt) outliers start: 15 outliers final: 10 residues processed: 85 average time/residue: 0.1317 time to fit residues: 14.8627 Evaluate side-chains 83 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.0570 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 30.0000 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4378 Z= 0.189 Angle : 0.572 7.286 5951 Z= 0.281 Chirality : 0.040 0.188 695 Planarity : 0.003 0.033 726 Dihedral : 6.594 72.446 680 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.41 % Allowed : 20.44 % Favored : 76.16 % 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: 1.13 (0.37), residues: 562 helix: 1.82 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -1.08 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 171 HIS 0.004 0.001 HIS A 92 PHE 0.011 0.001 PHE A 591 TYR 0.024 0.001 TYR A 590 ARG 0.007 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8849 (tpt) cc_final: 0.8516 (tpp) REVERT: A 170 MET cc_start: 0.7475 (mmm) cc_final: 0.7171 (mmm) REVERT: A 254 TRP cc_start: 0.7606 (t-100) cc_final: 0.7308 (t60) REVERT: A 381 ILE cc_start: 0.8736 (tp) cc_final: 0.8414 (tp) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.1489 time to fit residues: 17.1397 Evaluate side-chains 88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 340 MET Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 27 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 43 optimal weight: 50.0000 chunk 49 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 48 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4378 Z= 0.163 Angle : 0.552 7.211 5951 Z= 0.271 Chirality : 0.040 0.188 695 Planarity : 0.003 0.032 726 Dihedral : 6.390 68.933 680 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.89 % Allowed : 19.95 % Favored : 76.16 % 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: 1.26 (0.37), residues: 562 helix: 1.90 (0.29), residues: 350 sheet: None (None), residues: 0 loop : -1.02 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 602 HIS 0.004 0.001 HIS A 92 PHE 0.009 0.001 PHE A 591 TYR 0.024 0.001 TYR A 590 ARG 0.006 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8804 (tpt) cc_final: 0.8491 (tpp) REVERT: A 170 MET cc_start: 0.7415 (mmm) cc_final: 0.7130 (mmt) REVERT: A 176 MET cc_start: 0.8069 (tpp) cc_final: 0.7613 (tpp) REVERT: A 254 TRP cc_start: 0.7639 (t-100) cc_final: 0.7334 (t60) REVERT: A 356 PHE cc_start: 0.7222 (m-80) cc_final: 0.6635 (t80) REVERT: A 381 ILE cc_start: 0.8731 (tp) cc_final: 0.8414 (tp) outliers start: 16 outliers final: 12 residues processed: 89 average time/residue: 0.1366 time to fit residues: 16.1429 Evaluate side-chains 86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 22 optimal weight: 0.2980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 0.0770 chunk 51 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4378 Z= 0.171 Angle : 0.562 7.086 5951 Z= 0.276 Chirality : 0.041 0.191 695 Planarity : 0.003 0.030 726 Dihedral : 6.253 67.263 680 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.41 % Allowed : 21.17 % Favored : 75.43 % 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: 1.34 (0.37), residues: 562 helix: 1.96 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -0.95 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 602 HIS 0.004 0.001 HIS A 92 PHE 0.013 0.001 PHE A 427 TYR 0.024 0.001 TYR A 590 ARG 0.007 0.001 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8811 (tpt) cc_final: 0.8487 (tpp) REVERT: A 176 MET cc_start: 0.8088 (tpp) cc_final: 0.7641 (tpp) REVERT: A 254 TRP cc_start: 0.7684 (t-100) cc_final: 0.7312 (t60) REVERT: A 356 PHE cc_start: 0.7240 (m-80) cc_final: 0.6645 (t80) REVERT: A 381 ILE cc_start: 0.8734 (tp) cc_final: 0.8413 (tp) REVERT: A 598 THR cc_start: 0.8876 (p) cc_final: 0.8615 (t) outliers start: 14 outliers final: 12 residues processed: 87 average time/residue: 0.1474 time to fit residues: 17.1186 Evaluate side-chains 90 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 48 optimal weight: 0.0010 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.3626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4378 Z= 0.194 Angle : 0.573 7.367 5951 Z= 0.281 Chirality : 0.042 0.296 695 Planarity : 0.003 0.032 726 Dihedral : 6.191 67.470 680 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.16 % Allowed : 21.17 % Favored : 75.67 % 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: 1.39 (0.36), residues: 562 helix: 1.99 (0.29), residues: 348 sheet: None (None), residues: 0 loop : -0.91 (0.42), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 171 HIS 0.004 0.001 HIS A 92 PHE 0.011 0.001 PHE A 83 TYR 0.023 0.001 TYR A 590 ARG 0.007 0.001 ARG A 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1124 Ramachandran restraints generated. 562 Oldfield, 0 Emsley, 562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8825 (tpt) cc_final: 0.8499 (tpp) REVERT: A 176 MET cc_start: 0.8068 (tpp) cc_final: 0.7622 (tpp) REVERT: A 356 PHE cc_start: 0.7241 (m-80) cc_final: 0.6661 (t80) REVERT: A 381 ILE cc_start: 0.8761 (tp) cc_final: 0.8436 (tp) REVERT: A 598 THR cc_start: 0.8890 (p) cc_final: 0.8634 (t) outliers start: 13 outliers final: 13 residues processed: 84 average time/residue: 0.1408 time to fit residues: 15.7762 Evaluate side-chains 86 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 422 TYR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 612 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.2980 chunk 51 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.167627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.121603 restraints weight = 4821.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.118996 restraints weight = 4003.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.120488 restraints weight = 3946.524| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4378 Z= 0.208 Angle : 0.593 7.276 5951 Z= 0.294 Chirality : 0.042 0.270 695 Planarity : 0.003 0.024 726 Dihedral : 6.199 68.405 680 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.16 % Allowed : 21.65 % Favored : 75.18 % 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: 1.39 (0.36), residues: 562 helix: 1.99 (0.28), residues: 349 sheet: None (None), residues: 0 loop : -0.92 (0.41), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 171 HIS 0.004 0.001 HIS A 92 PHE 0.011 0.001 PHE A 427 TYR 0.023 0.001 TYR A 590 ARG 0.004 0.001 ARG A 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1242.47 seconds wall clock time: 23 minutes 33.00 seconds (1413.00 seconds total)