Starting phenix.real_space_refine on Thu Mar 6 00:40:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6l_36922/03_2025/8k6l_36922.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6l_36922/03_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_36922/03_2025/8k6l_36922.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6l_36922/03_2025/8k6l_36922.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6l_36922/03_2025/8k6l_36922.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6l_36922/03_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-5624/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: 3.35, per 1000 atoms: 0.81 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: 1.06 Conformation dependent library (CDL) restraints added in 509.2 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: 0.46 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: 1.38 Time building geometry restraints manager: 1.27 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: 1.540 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: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.160 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:31.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.450 ------------------------------------------------------------------------------- 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 : 0.394 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: 1.1439 time to fit residues: 98.6266 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 : 0.445 ------------------------------------------------------------------------------- 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: 2.88 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: 0.7715 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 : 0.390 Fit side-chains REVERT: A 48 MET cc_start: 0.7236 (tpt) cc_final: 0.7020 (tpp) REVERT: A 74 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7955 (mm-30) REVERT: A 185 GLU cc_start: 0.8346 (pt0) cc_final: 0.7979 (pp20) REVERT: A 198 ASP cc_start: 0.8287 (m-30) cc_final: 0.7755 (m-30) REVERT: A 226 LEU cc_start: 0.6446 (pp) cc_final: 0.6173 (mt) REVERT: A 253 ARG cc_start: 0.7811 (mtm180) cc_final: 0.6014 (mtp-110) REVERT: A 580 ARG cc_start: 0.8027 (mtp-110) cc_final: 0.7468 (mtm-85) REVERT: A 648 LYS cc_start: 0.7340 (ttmt) cc_final: 0.6571 (ttpt) outliers start: 12 outliers final: 3 residues processed: 65 average time/residue: 1.1992 time to fit residues: 81.1889 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 : 0.450 ------------------------------------------------------------------------------- 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 = 0.3740 r_free = 0.3740 target = 0.153519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115067 restraints weight = 4980.264| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.17 r_work: 0.3186 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2317 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= 0.189 Angle : 0.588 7.663 5782 Z= 0.303 Chirality : 0.052 0.680 678 Planarity : 0.004 0.049 700 Dihedral : 6.983 58.844 660 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.37 % Allowed : 19.76 % 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: 0.51 (0.37), residues: 539 helix: 1.50 (0.29), residues: 344 sheet: None (None), residues: 0 loop : -1.87 (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 0.025 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 63 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 176 MET cc_start: 0.7572 (mmm) cc_final: 0.7362 (mmt) REVERT: A 198 ASP cc_start: 0.8247 (m-30) cc_final: 0.7556 (m-30) REVERT: A 253 ARG cc_start: 0.7816 (mtm180) cc_final: 0.5960 (mtp-110) REVERT: A 348 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7254 (tp-100) REVERT: A 623 ARG cc_start: 0.7402 (tpp80) cc_final: 0.7021 (mtt180) REVERT: A 648 LYS cc_start: 0.7234 (ttmt) cc_final: 0.6518 (ttpt) outliers start: 14 outliers final: 3 residues processed: 58 average time/residue: 0.9921 time to fit residues: 60.1577 Evaluate side-chains 52 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 0.0000 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.6586 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.152220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.114242 restraints weight = 4935.109| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.16 r_work: 0.3160 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2558 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= 0.183 Angle : 0.561 7.215 5782 Z= 0.288 Chirality : 0.050 0.664 678 Planarity : 0.004 0.049 700 Dihedral : 6.594 52.781 660 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.13 % Allowed : 20.72 % 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: 0.94 (0.37), residues: 539 helix: 1.74 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.51 (0.42), residues: 194 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 0.015 0.001 PHE A 501 TYR 0.023 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 64 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.536 Fit side-chains REVERT: A 185 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7937 (pp20) REVERT: A 198 ASP cc_start: 0.8266 (m-30) cc_final: 0.7598 (m-30) REVERT: A 253 ARG cc_start: 0.7810 (mtm180) cc_final: 0.5961 (mtp-110) REVERT: A 348 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7250 (tp-100) REVERT: A 623 ARG cc_start: 0.7359 (tpp80) cc_final: 0.6962 (mtt180) REVERT: A 648 LYS cc_start: 0.7127 (ttmt) cc_final: 0.6419 (ttpt) outliers start: 13 outliers final: 7 residues processed: 60 average time/residue: 1.1551 time to fit residues: 72.2894 Evaluate side-chains 57 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 636 SER 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: 4.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3722 r_free = 0.3722 target = 0.150298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.110584 restraints weight = 5065.189| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.42 r_work: 0.3130 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2681 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= 0.224 Angle : 0.576 7.338 5782 Z= 0.298 Chirality : 0.050 0.633 678 Planarity : 0.004 0.048 700 Dihedral : 6.675 55.494 660 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.37 % Allowed : 20.72 % Favored : 75.90 % 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: 1.05 (0.37), residues: 539 helix: 1.92 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.55 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 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 62 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.467 Fit side-chains REVERT: A 185 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: A 198 ASP cc_start: 0.8475 (m-30) cc_final: 0.7801 (m-30) REVERT: A 253 ARG cc_start: 0.7921 (mtm180) cc_final: 0.6099 (mtp-110) REVERT: A 348 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7613 (tp-100) REVERT: A 623 ARG cc_start: 0.7653 (tpp80) cc_final: 0.7262 (mtt180) REVERT: A 648 LYS cc_start: 0.7412 (ttmt) cc_final: 0.6714 (ttpt) outliers start: 14 outliers final: 6 residues processed: 58 average time/residue: 1.0107 time to fit residues: 61.4005 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 : 0.415 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 49 optimal weight: 0.9990 chunk 18 optimal weight: 0.0470 chunk 38 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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 = 0.3771 r_free = 0.3771 target = 0.154005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.114552 restraints weight = 4986.318| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.42 r_work: 0.3190 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4258 Z= 0.163 Angle : 0.537 6.880 5782 Z= 0.275 Chirality : 0.048 0.628 678 Planarity : 0.004 0.048 700 Dihedral : 6.548 54.030 660 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.37 % Allowed : 21.45 % 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: 1.30 (0.37), residues: 539 helix: 2.14 (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 0.004 0.001 TRP A 171 HIS 0.002 0.001 HIS A 115 PHE 0.015 0.001 PHE A 501 TYR 0.023 0.001 TYR A 590 ARG 0.001 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 61 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.442 Fit side-chains REVERT: A 198 ASP cc_start: 0.8599 (m-30) cc_final: 0.7978 (m-30) REVERT: A 247 ILE cc_start: 0.8627 (pt) cc_final: 0.8360 (tp) REVERT: A 253 ARG cc_start: 0.7973 (mtm180) cc_final: 0.6181 (mtp-110) REVERT: A 348 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7674 (tp-100) REVERT: A 623 ARG cc_start: 0.7673 (tpp80) cc_final: 0.7358 (mtt180) REVERT: A 648 LYS cc_start: 0.7277 (ttmt) cc_final: 0.6568 (ttpt) outliers start: 14 outliers final: 7 residues processed: 57 average time/residue: 1.0230 time to fit residues: 60.8721 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 : 0.362 ------------------------------------------------------------------------------- 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 474 CYS Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 560 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 30 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.151982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.112425 restraints weight = 4967.367| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.38 r_work: 0.3154 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2902 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= 0.209 Angle : 0.575 8.251 5782 Z= 0.297 Chirality : 0.049 0.619 678 Planarity : 0.004 0.048 700 Dihedral : 6.717 54.535 660 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.37 % Allowed : 20.48 % 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: 1.22 (0.37), residues: 539 helix: 2.11 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.59 (0.41), 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 0.017 0.001 PHE A 386 TYR 0.022 0.001 TYR A 625 ARG 0.002 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 62 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.407 Fit side-chains REVERT: A 198 ASP cc_start: 0.8644 (m-30) cc_final: 0.7978 (m-30) REVERT: A 247 ILE cc_start: 0.8636 (pt) cc_final: 0.8309 (tp) REVERT: A 348 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7795 (tp-100) REVERT: A 623 ARG cc_start: 0.7716 (tpp80) cc_final: 0.7335 (mtt180) REVERT: A 648 LYS cc_start: 0.7394 (ttmt) cc_final: 0.6686 (ttpt) outliers start: 14 outliers final: 8 residues processed: 59 average time/residue: 1.1868 time to fit residues: 72.8438 Evaluate side-chains 56 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.433 ------------------------------------------------------------------------------- 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: 0.1980 chunk 7 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.152943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.113193 restraints weight = 4899.128| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 2.39 r_work: 0.3161 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3054 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= 0.184 Angle : 0.558 8.051 5782 Z= 0.288 Chirality : 0.049 0.607 678 Planarity : 0.004 0.048 700 Dihedral : 6.706 57.349 660 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.89 % Allowed : 22.17 % Favored : 74.94 % 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: 1.33 (0.37), residues: 539 helix: 2.20 (0.29), residues: 339 sheet: None (None), residues: 0 loop : -1.55 (0.41), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 254 HIS 0.005 0.001 HIS A 520 PHE 0.015 0.001 PHE A 386 TYR 0.022 0.001 TYR A 590 ARG 0.002 0.000 ARG A 633 *********************** 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 62 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.455 Fit side-chains REVERT: A 198 ASP cc_start: 0.8612 (m-30) cc_final: 0.7945 (m-30) REVERT: A 247 ILE cc_start: 0.8658 (pt) cc_final: 0.8382 (tp) REVERT: A 253 ARG cc_start: 0.7950 (mtm180) cc_final: 0.6142 (mtp-110) REVERT: A 348 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7722 (tp-100) REVERT: A 440 MET cc_start: 0.8169 (ptm) cc_final: 0.7925 (ptt) REVERT: A 521 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7701 (mm) REVERT: A 623 ARG cc_start: 0.7680 (tpp80) cc_final: 0.7306 (mtt180) REVERT: A 648 LYS cc_start: 0.7298 (ttmt) cc_final: 0.6573 (ttpt) outliers start: 12 outliers final: 9 residues processed: 58 average time/residue: 1.4101 time to fit residues: 85.2804 Evaluate side-chains 63 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 521 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 34 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 10 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.151922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112230 restraints weight = 4953.325| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.39 r_work: 0.3146 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3082 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= 0.192 Angle : 0.564 9.285 5782 Z= 0.290 Chirality : 0.048 0.608 678 Planarity : 0.004 0.049 700 Dihedral : 6.680 59.127 660 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.89 % Allowed : 22.41 % Favored : 74.70 % 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 (0.37), residues: 539 helix: 2.23 (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 0.004 0.001 TRP A 254 HIS 0.002 0.001 HIS A 115 PHE 0.017 0.001 PHE A 386 TYR 0.022 0.001 TYR A 625 ARG 0.002 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 63 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 198 ASP cc_start: 0.8627 (m-30) cc_final: 0.7968 (m-30) REVERT: A 247 ILE cc_start: 0.8701 (pt) cc_final: 0.8351 (tp) REVERT: A 251 ASP cc_start: 0.7286 (m-30) cc_final: 0.6912 (m-30) REVERT: A 348 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7769 (tp-100) REVERT: A 417 MET cc_start: 0.8908 (tpp) cc_final: 0.8613 (mmm) REVERT: A 440 MET cc_start: 0.8134 (ptm) cc_final: 0.7932 (ptt) REVERT: A 521 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7696 (mm) REVERT: A 623 ARG cc_start: 0.7684 (tpp80) cc_final: 0.7321 (mtt180) REVERT: A 648 LYS cc_start: 0.7313 (ttmt) cc_final: 0.6587 (ttpt) outliers start: 12 outliers final: 8 residues processed: 58 average time/residue: 1.0158 time to fit residues: 61.6189 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 : 0.463 ------------------------------------------------------------------------------- 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 521 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=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: 0.6980 chunk 36 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.0060 chunk 43 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3778 r_free = 0.3778 target = 0.154084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.115117 restraints weight = 4956.662| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.37 r_work: 0.3178 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4258 Z= 0.167 Angle : 0.550 9.400 5782 Z= 0.282 Chirality : 0.048 0.602 678 Planarity : 0.004 0.050 700 Dihedral : 6.546 55.819 660 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.89 % Allowed : 22.17 % Favored : 74.94 % 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: 1.47 (0.38), residues: 539 helix: 2.21 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.41 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 258 HIS 0.002 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 ********************** 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 60 residues out of total 473 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.475 Fit side-chains REVERT: A 198 ASP cc_start: 0.8606 (m-30) cc_final: 0.7957 (m-30) REVERT: A 247 ILE cc_start: 0.8696 (pt) cc_final: 0.8375 (tp) REVERT: A 251 ASP cc_start: 0.7233 (m-30) cc_final: 0.6864 (m-30) REVERT: A 253 ARG cc_start: 0.7953 (mtm180) cc_final: 0.6048 (mmm160) REVERT: A 348 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7686 (tp-100) REVERT: A 417 MET cc_start: 0.8835 (tpp) cc_final: 0.8560 (mmm) REVERT: A 521 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7674 (mm) outliers start: 12 outliers final: 6 residues processed: 55 average time/residue: 1.0065 time to fit residues: 58.0476 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 : 0.446 ------------------------------------------------------------------------------- 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 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: 0.0070 chunk 32 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 37 optimal weight: 0.0050 chunk 34 optimal weight: 0.0870 chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.157394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.118619 restraints weight = 4948.254| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.39 r_work: 0.3234 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4258 Z= 0.142 Angle : 0.531 9.539 5782 Z= 0.270 Chirality : 0.047 0.596 678 Planarity : 0.004 0.051 700 Dihedral : 6.089 53.302 659 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.45 % Allowed : 23.86 % Favored : 74.70 % 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: 1.65 (0.38), residues: 539 helix: 2.34 (0.29), residues: 345 sheet: None (None), residues: 0 loop : -1.33 (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 0.024 0.001 TYR A 590 ARG 0.001 0.000 ARG A 181 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3465.71 seconds wall clock time: 61 minutes 41.48 seconds (3701.48 seconds total)