Starting phenix.real_space_refine on Fri Dec 27 12:44:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bvr_16269/12_2024/8bvr_16269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bvr_16269/12_2024/8bvr_16269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bvr_16269/12_2024/8bvr_16269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bvr_16269/12_2024/8bvr_16269.map" model { file = "/net/cci-nas-00/data/ceres_data/8bvr_16269/12_2024/8bvr_16269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bvr_16269/12_2024/8bvr_16269.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.054 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 P 3 5.49 5 S 35 5.16 5 C 3100 2.51 5 N 812 2.21 5 O 856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 4806 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3896 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 502, 3884 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 25, 'TRANS': 476} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 502, 3884 Classifications: {'peptide': 502} Link IDs: {'PTRANS': 25, 'TRANS': 476} Chain breaks: 2 bond proxies already assigned to first conformer: 3962 Chain: "B" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 895 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 15 Unusual residues: {'PO4': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 230 " occ=0.68 ... (22 atoms not shown) pdb=" OH BTYR A 230 " occ=0.32 Time building chain proxies: 5.38, per 1000 atoms: 1.12 Number of scatterers: 4806 At special positions: 0 Unit cell: (114.816, 69.888, 81.536, 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) S 35 16.00 P 3 15.00 O 856 8.00 N 812 7.00 C 3100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 105 " distance=2.03 Simple disulfide: pdb=" SG CYS A 78 " - pdb=" SG CYS A 128 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 1.1 seconds 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1136 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 66.3% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 14 through 26 Processing helix chain 'A' and resid 27 through 42 removed outlier: 4.433A pdb=" N GLN A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN A 39 " --> pdb=" O ASN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 61 removed outlier: 3.721A pdb=" N GLY A 61 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 125 Processing helix chain 'A' and resid 130 through 160 removed outlier: 4.072A pdb=" N ARG A 134 " --> pdb=" O HIS A 130 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN A 135 " --> pdb=" O ARG A 131 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 181 Processing helix chain 'A' and resid 184 through 214 removed outlier: 3.712A pdb=" N TYR A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 218 through 244 Processing helix chain 'A' and resid 247 through 265 Proline residue: A 257 - end of helix removed outlier: 3.608A pdb=" N ILE A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 271 through 278 removed outlier: 3.552A pdb=" N TYR A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 298 through 304 removed outlier: 3.718A pdb=" N LEU A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 removed outlier: 3.985A pdb=" N ARG A 310 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 311 " --> pdb=" O GLU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 Processing helix chain 'A' and resid 326 through 332 removed outlier: 4.197A pdb=" N CYS A 332 " --> pdb=" O GLU A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 358 removed outlier: 3.904A pdb=" N MET A 358 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.549A pdb=" N GLY A 362 " --> pdb=" O ASP A 359 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE A 363 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY A 364 " --> pdb=" O GLN A 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 364' Processing helix chain 'A' and resid 366 through 392 removed outlier: 4.409A pdb=" N LEU A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 394 through 415 Processing helix chain 'A' and resid 420 through 449 removed outlier: 3.657A pdb=" N GLY A 432 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 Proline residue: A 473 - end of helix removed outlier: 3.746A pdb=" N THR A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 502 Proline residue: A 494 - end of helix Processing helix chain 'A' and resid 516 through 526 removed outlier: 4.362A pdb=" N LYS A 520 " --> pdb=" O VAL A 516 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 521 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 removed outlier: 3.756A pdb=" N GLY B 55 " --> pdb=" O TRP B 52 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.503A pdb=" N HIS A 48 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 80 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.613A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 21 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N MET B 83 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N CYS B 22 " --> pdb=" O VAL B 79 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL B 79 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 59 through 60 removed outlier: 4.072A pdb=" N ARG B 59 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR B 109 " --> pdb=" O TYR B 94 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 862 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: 1.36 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1510 1.34 - 1.46: 1165 1.46 - 1.58: 2188 1.58 - 1.70: 1 1.70 - 1.81: 55 Bond restraints: 4919 Sorted by residual: bond pdb=" CB PRO B 28 " pdb=" CG PRO B 28 " ideal model delta sigma weight residual 1.492 1.655 -0.163 5.00e-02 4.00e+02 1.06e+01 bond pdb=" O3 PO4 A 601 " pdb=" P PO4 A 601 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" O3 PO4 A 602 " pdb=" P PO4 A 602 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.81e+00 bond pdb=" O4 PO4 A 602 " pdb=" P PO4 A 602 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.62e+00 ... (remaining 4914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 6569 2.23 - 4.47: 92 4.47 - 6.70: 21 6.70 - 8.93: 2 8.93 - 11.16: 6 Bond angle restraints: 6690 Sorted by residual: angle pdb=" CA PRO B 28 " pdb=" N PRO B 28 " pdb=" CD PRO B 28 " ideal model delta sigma weight residual 112.00 100.84 11.16 1.40e+00 5.10e-01 6.36e+01 angle pdb=" O SER B 114 " pdb=" C SER B 114 " pdb=" N ALA B 115 " ideal model delta sigma weight residual 121.20 113.53 7.67 1.61e+00 3.86e-01 2.27e+01 angle pdb=" N PRO B 28 " pdb=" CD PRO B 28 " pdb=" CG PRO B 28 " ideal model delta sigma weight residual 103.20 97.15 6.05 1.50e+00 4.44e-01 1.63e+01 angle pdb=" C LEU A 288 " pdb=" N GLN A 289 " pdb=" CA GLN A 289 " ideal model delta sigma weight residual 121.14 114.50 6.64 1.75e+00 3.27e-01 1.44e+01 angle pdb=" CA LEU A 285 " pdb=" CB LEU A 285 " pdb=" CG LEU A 285 " ideal model delta sigma weight residual 116.30 126.43 -10.13 3.50e+00 8.16e-02 8.37e+00 ... (remaining 6685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 2429 17.65 - 35.29: 362 35.29 - 52.93: 84 52.93 - 70.58: 12 70.58 - 88.22: 4 Dihedral angle restraints: 2891 sinusoidal: 1113 harmonic: 1778 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 176.02 -83.02 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS A 49 " pdb=" SG CYS A 49 " pdb=" SG CYS A 105 " pdb=" CB CYS A 105 " ideal model delta sinusoidal sigma weight residual -86.00 -126.47 40.47 1 1.00e+01 1.00e-02 2.30e+01 dihedral pdb=" CB CYS A 78 " pdb=" SG CYS A 78 " pdb=" SG CYS A 128 " pdb=" CB CYS A 128 " ideal model delta sinusoidal sigma weight residual -86.00 -45.58 -40.42 1 1.00e+01 1.00e-02 2.29e+01 ... (remaining 2888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 594 0.045 - 0.090: 133 0.090 - 0.134: 31 0.134 - 0.179: 4 0.179 - 0.224: 1 Chirality restraints: 763 Sorted by residual: chirality pdb=" CG LEU A 285 " pdb=" CB LEU A 285 " pdb=" CD1 LEU A 285 " pdb=" CD2 LEU A 285 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA GLN A 289 " pdb=" N GLN A 289 " pdb=" C GLN A 289 " pdb=" CB GLN A 289 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.72e-01 chirality pdb=" CB THR A 22 " pdb=" CA THR A 22 " pdb=" OG1 THR A 22 " pdb=" CG2 THR A 22 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.63e-01 ... (remaining 760 not shown) Planarity restraints: 833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " 0.041 2.00e-02 2.50e+03 7.75e-02 6.00e+01 pdb=" C SER B 114 " -0.134 2.00e-02 2.50e+03 pdb=" O SER B 114 " 0.049 2.00e-02 2.50e+03 pdb=" N ALA B 115 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 27 " 0.039 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO B 28 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 116 " -0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 117 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " -0.027 5.00e-02 4.00e+02 ... (remaining 830 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 235 2.72 - 3.27: 4986 3.27 - 3.81: 8313 3.81 - 4.36: 9269 4.36 - 4.90: 16024 Nonbonded interactions: 38827 Sorted by model distance: nonbonded pdb=" O MET A 23 " pdb=" OH TYR A 264 " model vdw 2.178 3.040 nonbonded pdb=" O LYS A 71 " pdb=" NH1 ARG B 59 " model vdw 2.182 3.120 nonbonded pdb=" OG SER B 71 " pdb=" O TYR B 80 " model vdw 2.205 3.040 nonbonded pdb=" O PHE A 133 " pdb=" OH TYR A 185 " model vdw 2.221 3.040 nonbonded pdb=" O GLY A 446 " pdb=" NH1 ARG A 454 " model vdw 2.238 3.120 ... (remaining 38822 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=0.32 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.150 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.230 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.040 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 0.163 4919 Z= 0.318 Angle : 0.723 11.163 6690 Z= 0.357 Chirality : 0.041 0.224 763 Planarity : 0.006 0.077 833 Dihedral : 17.012 88.224 1746 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.19 % Allowed : 36.50 % Favored : 63.30 % 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: 0.64 (0.36), residues: 612 helix: 1.31 (0.28), residues: 361 sheet: -1.19 (0.84), residues: 41 loop : -0.71 (0.46), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 33 HIS 0.003 0.001 HIS A 34 PHE 0.017 0.001 PHE B 27 TYR 0.014 0.001 TYR A 275 ARG 0.004 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.655 Fit side-chains REVERT: B 51 ILE cc_start: 0.8414 (mp) cc_final: 0.7922 (pt) outliers start: 1 outliers final: 0 residues processed: 97 average time/residue: 0.1662 time to fit residues: 20.7523 Evaluate side-chains 95 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 24 optimal weight: 0.0270 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN A 439 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.0785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 4919 Z= 0.228 Angle : 0.675 9.296 6690 Z= 0.328 Chirality : 0.041 0.176 763 Planarity : 0.005 0.046 833 Dihedral : 3.978 14.177 675 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.24 % Allowed : 30.29 % Favored : 64.47 % 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: 0.85 (0.36), residues: 612 helix: 1.44 (0.28), residues: 367 sheet: -1.18 (0.82), residues: 47 loop : -0.57 (0.47), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 33 HIS 0.003 0.001 HIS A 34 PHE 0.015 0.001 PHE B 27 TYR 0.018 0.001 TYR A 264 ARG 0.006 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 99 time to evaluate : 0.547 Fit side-chains REVERT: A 5 ASP cc_start: 0.8203 (t0) cc_final: 0.7988 (t0) REVERT: A 135 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7333 (mm-40) REVERT: A 307 GLU cc_start: 0.8535 (mp0) cc_final: 0.8192 (pm20) REVERT: B 51 ILE cc_start: 0.8437 (mp) cc_final: 0.7963 (pt) outliers start: 27 outliers final: 16 residues processed: 117 average time/residue: 0.1513 time to fit residues: 23.3987 Evaluate side-chains 108 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 399 MET Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 55 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4919 Z= 0.206 Angle : 0.668 10.369 6690 Z= 0.317 Chirality : 0.040 0.150 763 Planarity : 0.005 0.044 833 Dihedral : 3.938 13.214 675 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 4.66 % Allowed : 30.68 % Favored : 64.66 % 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: 0.89 (0.36), residues: 612 helix: 1.53 (0.28), residues: 368 sheet: -1.38 (0.76), residues: 49 loop : -0.59 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 247 HIS 0.003 0.001 HIS A 34 PHE 0.012 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.006 0.001 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.542 Fit side-chains revert: symmetry clash REVERT: A 135 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7288 (mm-40) REVERT: A 307 GLU cc_start: 0.8565 (mp0) cc_final: 0.8230 (pm20) outliers start: 24 outliers final: 17 residues processed: 110 average time/residue: 0.1441 time to fit residues: 21.0787 Evaluate side-chains 106 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4919 Z= 0.270 Angle : 0.678 9.712 6690 Z= 0.328 Chirality : 0.041 0.150 763 Planarity : 0.005 0.048 833 Dihedral : 3.998 15.911 675 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 6.60 % Allowed : 28.93 % Favored : 64.47 % 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: 0.99 (0.36), residues: 612 helix: 1.56 (0.28), residues: 372 sheet: -1.22 (0.79), residues: 47 loop : -0.53 (0.48), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 247 HIS 0.002 0.001 HIS A 130 PHE 0.017 0.002 PHE B 27 TYR 0.016 0.001 TYR A 264 ARG 0.005 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.530 Fit side-chains REVERT: A 135 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7332 (mm-40) REVERT: B 51 ILE cc_start: 0.8412 (mp) cc_final: 0.8140 (pt) REVERT: B 60 TYR cc_start: 0.7492 (m-80) cc_final: 0.6738 (m-10) outliers start: 34 outliers final: 26 residues processed: 115 average time/residue: 0.1380 time to fit residues: 21.3060 Evaluate side-chains 113 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4919 Z= 0.269 Angle : 0.683 9.985 6690 Z= 0.332 Chirality : 0.041 0.159 763 Planarity : 0.005 0.049 833 Dihedral : 4.052 15.054 675 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.80 % Allowed : 28.54 % Favored : 64.66 % 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: 0.89 (0.35), residues: 612 helix: 1.54 (0.28), residues: 372 sheet: -1.27 (0.80), residues: 47 loop : -0.73 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 247 HIS 0.003 0.001 HIS A 34 PHE 0.013 0.001 PHE A 351 TYR 0.016 0.001 TYR A 264 ARG 0.005 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.523 Fit side-chains REVERT: A 135 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: B 51 ILE cc_start: 0.8488 (mp) cc_final: 0.8234 (pt) REVERT: B 60 TYR cc_start: 0.7541 (m-80) cc_final: 0.6780 (m-10) outliers start: 35 outliers final: 26 residues processed: 117 average time/residue: 0.1455 time to fit residues: 22.5928 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4919 Z= 0.201 Angle : 0.676 10.219 6690 Z= 0.322 Chirality : 0.040 0.151 763 Planarity : 0.005 0.045 833 Dihedral : 3.995 13.513 675 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 6.80 % Allowed : 29.71 % Favored : 63.50 % 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: 1.01 (0.36), residues: 612 helix: 1.67 (0.28), residues: 372 sheet: -1.32 (0.78), residues: 47 loop : -0.71 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 33 HIS 0.004 0.001 HIS A 34 PHE 0.014 0.001 PHE B 68 TYR 0.016 0.001 TYR A 264 ARG 0.005 0.001 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 0.410 Fit side-chains REVERT: A 135 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7253 (mm-40) REVERT: B 51 ILE cc_start: 0.8450 (mp) cc_final: 0.8205 (pt) REVERT: B 59 ARG cc_start: 0.7085 (ttt180) cc_final: 0.6818 (ttt180) REVERT: B 60 TYR cc_start: 0.7422 (m-80) cc_final: 0.6658 (m-10) outliers start: 35 outliers final: 27 residues processed: 117 average time/residue: 0.1462 time to fit residues: 22.6074 Evaluate side-chains 118 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 0.0870 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4919 Z= 0.220 Angle : 0.676 10.273 6690 Z= 0.324 Chirality : 0.040 0.168 763 Planarity : 0.005 0.045 833 Dihedral : 3.957 13.947 675 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.60 % Allowed : 29.71 % Favored : 63.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.36), residues: 612 helix: 1.68 (0.28), residues: 371 sheet: -1.34 (0.79), residues: 47 loop : -0.71 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 33 HIS 0.004 0.001 HIS A 34 PHE 0.022 0.001 PHE B 27 TYR 0.016 0.001 TYR A 264 ARG 0.006 0.001 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.526 Fit side-chains REVERT: A 135 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7265 (mm-40) REVERT: B 51 ILE cc_start: 0.8467 (mp) cc_final: 0.8210 (pt) REVERT: B 59 ARG cc_start: 0.7100 (ttt180) cc_final: 0.6758 (ttt180) REVERT: B 60 TYR cc_start: 0.7474 (m-80) cc_final: 0.7208 (m-10) outliers start: 34 outliers final: 27 residues processed: 117 average time/residue: 0.1358 time to fit residues: 21.4377 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.2980 chunk 37 optimal weight: 0.0980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 54 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4919 Z= 0.209 Angle : 0.675 11.040 6690 Z= 0.322 Chirality : 0.040 0.170 763 Planarity : 0.005 0.044 833 Dihedral : 3.930 13.817 675 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.21 % Allowed : 30.10 % Favored : 63.69 % 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: 1.10 (0.36), residues: 612 helix: 1.75 (0.28), residues: 370 sheet: -1.35 (0.79), residues: 47 loop : -0.68 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 33 HIS 0.004 0.001 HIS A 34 PHE 0.014 0.001 PHE B 68 TYR 0.015 0.001 TYR A 264 ARG 0.006 0.001 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 92 time to evaluate : 0.534 Fit side-chains REVERT: A 135 GLN cc_start: 0.7643 (OUTLIER) cc_final: 0.7250 (mm-40) REVERT: B 51 ILE cc_start: 0.8466 (mp) cc_final: 0.8203 (pt) REVERT: B 60 TYR cc_start: 0.7448 (m-80) cc_final: 0.7222 (m-10) outliers start: 32 outliers final: 27 residues processed: 115 average time/residue: 0.1387 time to fit residues: 21.5363 Evaluate side-chains 120 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 57 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4919 Z= 0.225 Angle : 0.680 10.465 6690 Z= 0.326 Chirality : 0.040 0.169 763 Planarity : 0.005 0.045 833 Dihedral : 3.922 13.978 675 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.63 % Allowed : 30.87 % Favored : 63.50 % 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: 1.11 (0.36), residues: 612 helix: 1.76 (0.28), residues: 370 sheet: -1.33 (0.79), residues: 47 loop : -0.67 (0.46), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 47 HIS 0.004 0.001 HIS A 34 PHE 0.024 0.001 PHE B 27 TYR 0.015 0.001 TYR A 264 ARG 0.006 0.000 ARG A 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.524 Fit side-chains REVERT: A 135 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7280 (mm-40) REVERT: B 51 ILE cc_start: 0.8475 (mp) cc_final: 0.8203 (pt) REVERT: B 60 TYR cc_start: 0.7430 (m-80) cc_final: 0.7216 (m-10) outliers start: 29 outliers final: 27 residues processed: 113 average time/residue: 0.1393 time to fit residues: 21.1139 Evaluate side-chains 119 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.0060 chunk 48 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4919 Z= 0.198 Angle : 0.674 11.992 6690 Z= 0.322 Chirality : 0.040 0.172 763 Planarity : 0.005 0.043 833 Dihedral : 3.873 13.984 675 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.02 % Allowed : 30.29 % Favored : 63.69 % 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: 1.16 (0.36), residues: 612 helix: 1.78 (0.28), residues: 371 sheet: -1.38 (0.78), residues: 47 loop : -0.59 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 47 HIS 0.004 0.001 HIS A 34 PHE 0.015 0.001 PHE B 68 TYR 0.014 0.001 TYR A 264 ARG 0.006 0.000 ARG A 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1224 Ramachandran restraints generated. 612 Oldfield, 0 Emsley, 612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.529 Fit side-chains REVERT: A 135 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7244 (mm-40) REVERT: A 273 ARG cc_start: 0.7862 (tpp80) cc_final: 0.7629 (tpt-90) REVERT: B 51 ILE cc_start: 0.8360 (mp) cc_final: 0.8058 (pt) REVERT: B 60 TYR cc_start: 0.7426 (m-80) cc_final: 0.7198 (m-10) outliers start: 31 outliers final: 28 residues processed: 118 average time/residue: 0.1275 time to fit residues: 20.6011 Evaluate side-chains 121 residues out of total 513 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 309 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 386 PHE Chi-restraints excluded: chain A residue 387 LEU Chi-restraints excluded: chain A residue 414 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 444 TYR Chi-restraints excluded: chain A residue 467 VAL Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.1980 chunk 2 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.4437 r_free = 0.4437 target = 0.215311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.162904 restraints weight = 13543.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.169423 restraints weight = 5581.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.173990 restraints weight = 3231.881| |-----------------------------------------------------------------------------| r_work (final): 0.3998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4009 r_free = 0.4009 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4919 Z= 0.195 Angle : 0.673 11.547 6690 Z= 0.321 Chirality : 0.040 0.172 763 Planarity : 0.005 0.042 833 Dihedral : 3.833 13.838 675 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 6.21 % Allowed : 30.29 % Favored : 63.50 % 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: 1.17 (0.36), residues: 612 helix: 1.81 (0.28), residues: 370 sheet: -1.40 (0.79), residues: 47 loop : -0.62 (0.47), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 47 HIS 0.004 0.001 HIS A 34 PHE 0.024 0.001 PHE B 27 TYR 0.015 0.001 TYR A 264 ARG 0.006 0.000 ARG A 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1415.11 seconds wall clock time: 26 minutes 36.25 seconds (1596.25 seconds total)