Starting phenix.real_space_refine on Tue Feb 11 05:16:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6l_36922/02_2025/8k6l_36922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6l_36922/02_2025/8k6l_36922.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k6l_36922/02_2025/8k6l_36922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6l_36922/02_2025/8k6l_36922.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6l_36922/02_2025/8k6l_36922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6l_36922/02_2025/8k6l_36922.cif" } resolution = 2.92 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= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 34 5.16 5 Cl 2 4.86 5 C 2749 2.51 5 N 651 2.21 5 O 719 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4155 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4086 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 18, 'TRANS': 528} Chain breaks: 3 Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 234 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 8, 'ASP:plan': 4, 'GLU:plan': 3, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 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: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'IOQ': 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: 3.40, per 1000 atoms: 0.82 Number of scatterers: 4155 At special positions: 0 Unit cell: (65.24, 100.656, 87.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 34 16.00 O 719 8.00 N 651 7.00 C 2749 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=1.71 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 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 802 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 531.8 milliseconds 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 996 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 3 sheets defined 67.3% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 removed outlier: 3.662A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA A 33 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A 35 " --> pdb=" O LEU A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 71 through 88 removed outlier: 3.577A pdb=" N ILE A 75 " --> pdb=" O GLY A 71 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (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 111 removed outlier: 3.808A pdb=" N THR A 111 " --> pdb=" O GLY A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.173A pdb=" N PHE A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 185 Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.747A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER A 194 " --> pdb=" O PRO A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 4.516A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.844A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 228 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 272 removed outlier: 3.614A pdb=" N LEU A 263 " --> pdb=" O TRP A 259 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 278 removed outlier: 3.851A pdb=" N PHE A 276 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 3.810A pdb=" N ILE A 332 " --> pdb=" O SER A 328 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 367 removed outlier: 5.301A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 401 removed outlier: 3.630A pdb=" N GLY A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Proline residue: A 384 - end of helix removed outlier: 3.514A pdb=" N ILE A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 removed outlier: 3.876A pdb=" N PHE A 421 " --> pdb=" O MET A 417 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 423 " --> pdb=" O LEU A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 457 through 461 Processing helix chain 'A' and resid 527 through 550 removed outlier: 3.846A pdb=" N THR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 560 Processing helix chain 'A' and resid 567 through 583 Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 502 removed outlier: 3.594A pdb=" N PHE A 501 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.820A pdb=" N CYS A 599 " --> pdb=" O TYR A 616 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TYR A 616 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS A 601 " --> pdb=" O ARG A 614 " (cutoff:3.500A) 244 hydrogen bonds defined for protein. 711 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: 1.08 Time building geometry restraints manager: 1.23 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: 881 1.33 - 1.45: 1009 1.45 - 1.57: 2315 1.57 - 1.70: 0 1.70 - 1.82: 53 Bond restraints: 4258 Sorted by residual: bond pdb=" C THR A 186 " pdb=" N PRO A 187 " ideal model delta sigma weight residual 1.331 1.371 -0.039 7.90e-03 1.60e+04 2.44e+01 bond pdb=" C SER A 140 " pdb=" N THR A 141 " ideal model delta sigma weight residual 1.332 1.291 0.041 1.40e-02 5.10e+03 8.70e+00 bond pdb=" C PHE A 591 " pdb=" O PHE A 591 " ideal model delta sigma weight residual 1.237 1.210 0.026 1.17e-02 7.31e+03 5.05e+00 bond pdb=" C PRO A 588 " pdb=" O PRO A 588 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.16e-02 7.43e+03 4.98e+00 bond pdb=" C ILE A 589 " pdb=" O ILE A 589 " ideal model delta sigma weight residual 1.237 1.212 0.025 1.13e-02 7.83e+03 4.97e+00 ... (remaining 4253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 5574 2.40 - 4.79: 175 4.79 - 7.19: 21 7.19 - 9.59: 10 9.59 - 11.98: 2 Bond angle restraints: 5782 Sorted by residual: angle pdb=" C ILE A 585 " pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta sigma weight residual 111.30 101.87 9.43 9.60e-01 1.09e+00 9.65e+01 angle pdb=" N ILE A 52 " pdb=" CA ILE A 52 " pdb=" C ILE A 52 " ideal model delta sigma weight residual 110.62 117.58 -6.96 1.02e+00 9.61e-01 4.65e+01 angle pdb=" N ASN A 375 " pdb=" CA ASN A 375 " pdb=" C ASN A 375 " ideal model delta sigma weight residual 111.02 120.98 -9.96 1.52e+00 4.33e-01 4.30e+01 angle pdb=" C ALA A 32 " pdb=" N ALA A 33 " pdb=" CA ALA A 33 " ideal model delta sigma weight residual 120.28 129.02 -8.74 1.34e+00 5.57e-01 4.25e+01 angle pdb=" C THR A 186 " pdb=" N PRO A 187 " pdb=" CA PRO A 187 " ideal model delta sigma weight residual 121.00 113.85 7.15 1.16e+00 7.43e-01 3.80e+01 ... (remaining 5777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 2317 21.07 - 42.14: 131 42.14 - 63.21: 43 63.21 - 84.28: 4 84.28 - 105.35: 16 Dihedral angle restraints: 2511 sinusoidal: 947 harmonic: 1564 Sorted by residual: dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual -86.00 -157.45 71.45 1 1.00e+01 1.00e-02 6.55e+01 dihedral pdb=" CB CYS A 599 " pdb=" SG CYS A 599 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -155.91 69.91 1 1.00e+01 1.00e-02 6.30e+01 dihedral pdb=" C TYR A 590 " pdb=" N TYR A 590 " pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " ideal model delta harmonic sigma weight residual -122.60 -139.33 16.73 0 2.50e+00 1.60e-01 4.48e+01 ... (remaining 2508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 672 0.243 - 0.486: 2 0.486 - 0.729: 2 0.729 - 0.972: 1 0.972 - 1.215: 1 Chirality restraints: 678 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 -2.19 -0.21 2.00e-02 2.50e+03 1.13e+02 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 503 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.18 -1.22 2.00e-01 2.50e+01 3.69e+01 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.16e+01 ... (remaining 675 not shown) Planarity restraints: 702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG B 1 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.094 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.524 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " -0.310 2.00e-02 2.50e+03 2.61e-01 8.49e+02 pdb=" C7 NAG B 2 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " -0.189 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " 0.448 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 802 " 0.309 2.00e-02 2.50e+03 2.60e-01 8.48e+02 pdb=" C7 NAG A 802 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG A 802 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG A 802 " -0.448 2.00e-02 2.50e+03 pdb=" O7 NAG A 802 " 0.030 2.00e-02 2.50e+03 ... (remaining 699 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1278 2.82 - 3.34: 3822 3.34 - 3.86: 6400 3.86 - 4.38: 7155 4.38 - 4.90: 12360 Nonbonded interactions: 31015 Sorted by model distance: nonbonded pdb=" O SER A 85 " pdb=" OG SER A 89 " model vdw 2.297 3.040 nonbonded pdb=" O GLY A 324 " pdb=" OG SER A 328 " model vdw 2.387 3.040 nonbonded pdb=" O LEU A 507 " pdb=" CD1 LEU A 507 " model vdw 2.400 3.460 nonbonded pdb=" O SER A 491 " pdb=" CD1 PHE A 501 " model vdw 2.463 3.340 nonbonded pdb=" O SER A 371 " pdb=" OG SER A 371 " model vdw 2.475 3.040 ... (remaining 31010 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 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: 0.800 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.940 Find NCS groups from input model: 0.120 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:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 0.041 4258 Z= 0.345 Angle : 1.005 11.983 5782 Z= 0.659 Chirality : 0.086 1.215 678 Planarity : 0.019 0.294 700 Dihedral : 17.751 105.346 1494 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.17 % Allowed : 13.98 % Favored : 83.86 % Cbeta Deviations : 0.20 % 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: -2.44 (0.31), residues: 539 helix: -0.93 (0.25), residues: 333 sheet: None (None), residues: 0 loop : -2.71 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 171 HIS 0.002 0.001 HIS A 575 PHE 0.012 0.001 PHE A 621 TYR 0.026 0.002 TYR A 625 ARG 0.002 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.470 Fit side-chains REVERT: A 198 ASP cc_start: 0.8666 (m-30) cc_final: 0.8031 (m-30) REVERT: A 253 ARG cc_start: 0.7701 (mtm180) cc_final: 0.6301 (mtp-110) REVERT: A 580 ARG cc_start: 0.7790 (mtp-110) cc_final: 0.7566 (mtt90) REVERT: A 623 ARG cc_start: 0.7437 (tpp80) cc_final: 0.7188 (mtm-85) REVERT: A 648 LYS cc_start: 0.7736 (ttmt) cc_final: 0.6993 (ttpt) outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 1.0807 time to fit residues: 93.2019 Evaluate side-chains 59 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0000 chunk 40 optimal weight: 0.0170 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 27 optimal weight: 0.0070 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 overall best weight: 0.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.161884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122598 restraints weight = 4986.499| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.43 r_work: 0.3271 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4258 Z= 0.162 Angle : 0.648 8.203 5782 Z= 0.323 Chirality : 0.056 0.794 678 Planarity : 0.004 0.052 700 Dihedral : 9.039 53.304 662 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.89 % Allowed : 19.52 % Favored : 77.59 % 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: -0.24 (0.36), residues: 539 helix: 0.95 (0.29), residues: 342 sheet: None (None), residues: 0 loop : -2.22 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 171 HIS 0.002 0.001 HIS A 520 PHE 0.013 0.001 PHE A 501 TYR 0.025 0.001 TYR A 590 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.433 Fit side-chains REVERT: A 48 MET cc_start: 0.7233 (tpt) cc_final: 0.7017 (tpp) REVERT: A 74 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7955 (mm-30) REVERT: A 185 GLU cc_start: 0.8346 (pt0) cc_final: 0.7980 (pp20) REVERT: A 198 ASP cc_start: 0.8294 (m-30) cc_final: 0.7762 (m-30) REVERT: A 226 LEU cc_start: 0.6442 (pp) cc_final: 0.6171 (mt) REVERT: A 253 ARG cc_start: 0.7812 (mtm180) cc_final: 0.6016 (mtp-110) REVERT: A 580 ARG cc_start: 0.8030 (mtp-110) cc_final: 0.7473 (mtm-85) REVERT: A 648 LYS cc_start: 0.7343 (ttmt) cc_final: 0.6572 (ttpt) outliers start: 12 outliers final: 3 residues processed: 65 average time/residue: 1.1388 time to fit residues: 77.0426 Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 38 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 178 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.153663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115285 restraints weight = 4984.564| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.19 r_work: 0.3191 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4258 Z= 0.189 Angle : 0.586 7.667 5782 Z= 0.302 Chirality : 0.051 0.683 678 Planarity : 0.004 0.050 700 Dihedral : 6.978 58.421 660 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.86 % Allowed : 19.28 % Favored : 76.87 % 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 (0.37), residues: 539 helix: 1.49 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -1.89 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 258 HIS 0.002 0.001 HIS A 575 PHE 0.013 0.001 PHE A 621 TYR 0.024 0.002 TYR A 625 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.709 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.7530 (mmm) cc_final: 0.7319 (mmt) REVERT: A 198 ASP cc_start: 0.8231 (m-30) cc_final: 0.7592 (m-30) REVERT: A 253 ARG cc_start: 0.7810 (mtm180) cc_final: 0.5937 (mtp-110) REVERT: A 348 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7204 (tp-100) REVERT: A 482 ILE cc_start: 0.7996 (OUTLIER) cc_final: 0.7711 (mt) REVERT: A 648 LYS cc_start: 0.7221 (ttmt) cc_final: 0.6501 (ttpt) outliers start: 16 outliers final: 3 residues processed: 59 average time/residue: 0.9682 time to fit residues: 60.2250 Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 482 ILE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 37 optimal weight: 0.3980 chunk 17 optimal weight: 0.0670 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.154563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116447 restraints weight = 4942.611| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.18 r_work: 0.3215 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4258 Z= 0.159 Angle : 0.546 7.102 5782 Z= 0.279 Chirality : 0.049 0.659 678 Planarity : 0.004 0.050 700 Dihedral : 6.555 53.131 660 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.65 % Allowed : 21.20 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.37), residues: 539 helix: 1.90 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.60 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 171 HIS 0.001 0.001 HIS A 115 PHE 0.014 0.001 PHE A 501 TYR 0.024 0.001 TYR A 590 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.447 Fit side-chains REVERT: A 185 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7935 (pp20) REVERT: A 198 ASP cc_start: 0.8218 (m-30) cc_final: 0.7545 (m-30) REVERT: A 253 ARG cc_start: 0.7836 (mtm180) cc_final: 0.5984 (mtp-110) REVERT: A 348 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7159 (tp-100) REVERT: A 417 MET cc_start: 0.8621 (tpp) cc_final: 0.8391 (mmp) REVERT: A 648 LYS cc_start: 0.6906 (ttmt) cc_final: 0.6220 (ttpt) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 0.9879 time to fit residues: 59.0521 Evaluate side-chains 55 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 647 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.152106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112624 restraints weight = 5051.966| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.40 r_work: 0.3139 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4258 Z= 0.206 Angle : 0.571 7.308 5782 Z= 0.294 Chirality : 0.049 0.635 678 Planarity : 0.004 0.048 700 Dihedral : 6.615 55.066 660 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.13 % Allowed : 21.69 % 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: 1.15 (0.37), residues: 539 helix: 1.99 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.50 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.002 0.001 HIS A 520 PHE 0.014 0.001 PHE A 621 TYR 0.023 0.002 TYR A 625 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 0.441 Fit side-chains REVERT: A 185 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: A 198 ASP cc_start: 0.8146 (m-30) cc_final: 0.7426 (m-30) REVERT: A 253 ARG cc_start: 0.7792 (mtm180) cc_final: 0.5929 (mtp-110) REVERT: A 348 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7206 (tp-100) REVERT: A 417 MET cc_start: 0.8588 (tpp) cc_final: 0.8379 (mmp) REVERT: A 553 THR cc_start: 0.8248 (m) cc_final: 0.8031 (p) REVERT: A 623 ARG cc_start: 0.7328 (tpp80) cc_final: 0.6932 (mtt180) REVERT: A 648 LYS cc_start: 0.6957 (ttmt) cc_final: 0.6283 (ttpt) outliers start: 13 outliers final: 8 residues processed: 59 average time/residue: 1.0413 time to fit residues: 64.3569 Evaluate side-chains 59 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 185 GLU Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 647 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3753 r_free = 0.3753 target = 0.152028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112293 restraints weight = 4971.784| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.40 r_work: 0.3161 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4258 Z= 0.194 Angle : 0.556 6.980 5782 Z= 0.286 Chirality : 0.049 0.628 678 Planarity : 0.004 0.047 700 Dihedral : 6.605 54.389 660 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.86 % Allowed : 20.48 % Favored : 75.66 % 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: 1.25 (0.37), residues: 539 helix: 2.08 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.47 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 171 HIS 0.002 0.001 HIS A 520 PHE 0.014 0.001 PHE A 501 TYR 0.022 0.001 TYR A 625 ARG 0.002 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.470 Fit side-chains REVERT: A 198 ASP cc_start: 0.8613 (m-30) cc_final: 0.7944 (m-30) REVERT: A 247 ILE cc_start: 0.8635 (pt) cc_final: 0.8337 (tp) REVERT: A 253 ARG cc_start: 0.7942 (mtm180) cc_final: 0.6139 (mtp-110) REVERT: A 348 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7762 (tp-100) REVERT: A 417 MET cc_start: 0.8921 (tpp) cc_final: 0.8672 (mmp) REVERT: A 623 ARG cc_start: 0.7788 (tpp80) cc_final: 0.7438 (mtt180) REVERT: A 648 LYS cc_start: 0.7450 (ttmt) cc_final: 0.6747 (ttpt) outliers start: 16 outliers final: 7 residues processed: 60 average time/residue: 1.0357 time to fit residues: 64.9076 Evaluate side-chains 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 636 SER Chi-restraints excluded: chain A residue 647 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 0 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.0570 chunk 10 optimal weight: 0.0470 chunk 39 optimal weight: 7.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.155647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116296 restraints weight = 4958.170| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.44 r_work: 0.3185 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4258 Z= 0.159 Angle : 0.549 7.933 5782 Z= 0.283 Chirality : 0.048 0.618 678 Planarity : 0.004 0.048 700 Dihedral : 6.693 54.867 660 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.89 % Allowed : 20.96 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.38), residues: 539 helix: 2.26 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.54 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 171 HIS 0.002 0.001 HIS A 115 PHE 0.017 0.001 PHE A 386 TYR 0.023 0.001 TYR A 590 ARG 0.001 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.571 Fit side-chains REVERT: A 198 ASP cc_start: 0.8538 (m-30) cc_final: 0.7869 (m-30) REVERT: A 247 ILE cc_start: 0.8611 (pt) cc_final: 0.8339 (tp) REVERT: A 253 ARG cc_start: 0.7940 (mtm180) cc_final: 0.6130 (mtp-110) REVERT: A 348 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7560 (tp-100) REVERT: A 417 MET cc_start: 0.8824 (tpp) cc_final: 0.8603 (mmt) REVERT: A 648 LYS cc_start: 0.7073 (ttmt) cc_final: 0.6363 (ttpt) outliers start: 12 outliers final: 8 residues processed: 57 average time/residue: 1.0253 time to fit residues: 61.1597 Evaluate side-chains 54 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 647 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 32 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.155862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.116681 restraints weight = 4881.640| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.37 r_work: 0.3209 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4258 Z= 0.157 Angle : 0.540 8.123 5782 Z= 0.276 Chirality : 0.048 0.603 678 Planarity : 0.004 0.048 700 Dihedral : 6.649 58.754 660 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.65 % Allowed : 21.93 % Favored : 75.42 % 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: 1.51 (0.38), residues: 539 helix: 2.35 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.005 0.001 HIS A 520 PHE 0.015 0.001 PHE A 386 TYR 0.023 0.001 TYR A 590 ARG 0.001 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.355 Fit side-chains REVERT: A 198 ASP cc_start: 0.8584 (m-30) cc_final: 0.7964 (m-30) REVERT: A 247 ILE cc_start: 0.8648 (pt) cc_final: 0.8391 (tp) REVERT: A 253 ARG cc_start: 0.7966 (mtm180) cc_final: 0.6026 (mmm160) REVERT: A 348 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7638 (tp-100) REVERT: A 417 MET cc_start: 0.8848 (tpp) cc_final: 0.8581 (mmm) REVERT: A 521 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7720 (mm) REVERT: A 605 ASN cc_start: 0.6523 (t0) cc_final: 0.6310 (t0) outliers start: 11 outliers final: 6 residues processed: 56 average time/residue: 1.0308 time to fit residues: 60.3782 Evaluate side-chains 57 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 20.0000 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.153678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.114228 restraints weight = 4945.866| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.38 r_work: 0.3170 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4258 Z= 0.178 Angle : 0.553 9.619 5782 Z= 0.282 Chirality : 0.048 0.604 678 Planarity : 0.004 0.048 700 Dihedral : 6.627 59.743 660 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.41 % Allowed : 22.41 % 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: 1.54 (0.38), residues: 539 helix: 2.35 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.45 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.016 0.001 PHE A 386 TYR 0.022 0.001 TYR A 590 ARG 0.001 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.475 Fit side-chains REVERT: A 198 ASP cc_start: 0.8610 (m-30) cc_final: 0.7960 (m-30) REVERT: A 247 ILE cc_start: 0.8659 (pt) cc_final: 0.8377 (tp) REVERT: A 253 ARG cc_start: 0.7953 (mtm180) cc_final: 0.6003 (mmm160) REVERT: A 348 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7680 (tp-100) REVERT: A 417 MET cc_start: 0.8863 (tpp) cc_final: 0.8593 (mmm) REVERT: A 521 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7721 (mm) REVERT: A 605 ASN cc_start: 0.6517 (t0) cc_final: 0.6303 (t0) REVERT: A 623 ARG cc_start: 0.7724 (tpp80) cc_final: 0.7381 (mtt180) outliers start: 10 outliers final: 6 residues processed: 55 average time/residue: 1.0527 time to fit residues: 60.5060 Evaluate side-chains 58 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 44 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 0.0470 chunk 43 optimal weight: 0.8980 chunk 18 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.155310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115675 restraints weight = 4949.003| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.41 r_work: 0.3193 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4258 Z= 0.161 Angle : 0.544 9.793 5782 Z= 0.277 Chirality : 0.048 0.598 678 Planarity : 0.004 0.049 700 Dihedral : 6.505 55.177 660 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.93 % Allowed : 22.89 % 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: 1.56 (0.38), residues: 539 helix: 2.28 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.37 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 171 HIS 0.002 0.001 HIS A 115 PHE 0.017 0.001 PHE A 386 TYR 0.023 0.001 TYR A 590 ARG 0.001 0.000 ARG A 633 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1078 Ramachandran restraints generated. 539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.429 Fit side-chains REVERT: A 198 ASP cc_start: 0.8606 (m-30) cc_final: 0.7995 (m-30) REVERT: A 247 ILE cc_start: 0.8666 (pt) cc_final: 0.8401 (tp) REVERT: A 253 ARG cc_start: 0.8007 (mtm180) cc_final: 0.6044 (mmm160) REVERT: A 348 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7644 (tp-100) REVERT: A 417 MET cc_start: 0.8778 (tpp) cc_final: 0.8507 (mmm) REVERT: A 521 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7705 (mm) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.9886 time to fit residues: 57.0347 Evaluate side-chains 56 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.0020 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.3980 chunk 48 optimal weight: 0.0970 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.3786 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.156626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.117444 restraints weight = 4943.040| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 2.40 r_work: 0.3217 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3089 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4258 Z= 0.151 Angle : 0.538 9.712 5782 Z= 0.273 Chirality : 0.047 0.597 678 Planarity : 0.004 0.049 700 Dihedral : 6.077 53.375 659 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.69 % Allowed : 23.13 % 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: 1.66 (0.38), residues: 539 helix: 2.35 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.31 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.001 0.001 HIS A 115 PHE 0.018 0.001 PHE A 386 TYR 0.023 0.001 TYR A 590 ARG 0.001 0.000 ARG A 633 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3099.60 seconds wall clock time: 55 minutes 18.35 seconds (3318.35 seconds total)