Starting phenix.real_space_refine on Wed Jan 17 16:46:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvr_16269/01_2024/8bvr_16269.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvr_16269/01_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvr_16269/01_2024/8bvr_16269.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvr_16269/01_2024/8bvr_16269.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvr_16269/01_2024/8bvr_16269.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bvr_16269/01_2024/8bvr_16269.pdb" } 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 Residue "A ASP 5": "OD1" <-> "OD2" Residue "A ASP 107": "OD1" <-> "OD2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 4.82, per 1000 atoms: 1.00 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 - 3.50 Amino acid : False - 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: 1.79 Conformation dependent library (CDL) restraints added in 1.5 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: 0.49 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: 1.42 Time building geometry restraints manager: 1.95 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: 97.15 - 104.90: 97 104.90 - 112.65: 2592 112.65 - 120.40: 2051 120.40 - 128.15: 1905 128.15 - 135.91: 45 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 2.440 nonbonded pdb=" O LYS A 71 " pdb=" NH1 ARG B 59 " model vdw 2.182 2.520 nonbonded pdb=" OG SER B 71 " pdb=" O TYR B 80 " model vdw 2.205 2.440 nonbonded pdb=" O PHE A 133 " pdb=" OH TYR A 185 " model vdw 2.221 2.440 nonbonded pdb=" O GLY A 446 " pdb=" NH1 ARG A 454 " model vdw 2.238 2.520 ... (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 ========== 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: 1.290 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: 5.180 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.970 Find NCS groups from input model: 0.130 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: 0.010 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: 29.750 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.532 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: 0.1738 time to fit residues: 21.7742 Evaluate side-chains 95 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.607 ------------------------------------------------------------------------------- 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: 0.0070 chunk 46 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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: 0.7560 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 4919 Z= 0.207 Angle : 0.641 9.300 6690 Z= 0.309 Chirality : 0.040 0.170 763 Planarity : 0.004 0.045 833 Dihedral : 3.945 15.444 675 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.66 % Allowed : 31.07 % Favored : 64.27 % 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: 0.93 (0.36), residues: 612 helix: 1.52 (0.28), residues: 368 sheet: -1.18 (0.81), residues: 47 loop : -0.57 (0.48), residues: 197 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 0.013 0.001 TYR A 275 ARG 0.004 0.000 ARG A 395 *********************** 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 118 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 0.538 Fit side-chains REVERT: A 5 ASP cc_start: 0.8196 (t0) cc_final: 0.7986 (t0) REVERT: B 51 ILE cc_start: 0.8422 (mp) cc_final: 0.7948 (pt) outliers start: 24 outliers final: 15 residues processed: 111 average time/residue: 0.1514 time to fit residues: 22.0510 Evaluate side-chains 105 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL 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 282 ASP 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 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 109 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.0770 chunk 55 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 overall best weight: 0.8940 ------------------------------------------------------------------------------- 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: 0.7603 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4919 Z= 0.236 Angle : 0.657 9.818 6690 Z= 0.313 Chirality : 0.040 0.146 763 Planarity : 0.004 0.045 833 Dihedral : 3.896 14.633 675 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.63 % Allowed : 31.46 % Favored : 62.91 % 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: 0.95 (0.36), residues: 612 helix: 1.61 (0.28), residues: 368 sheet: -1.44 (0.76), residues: 49 loop : -0.63 (0.48), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 247 HIS 0.003 0.001 HIS A 47 PHE 0.014 0.001 PHE A 351 TYR 0.013 0.001 TYR A 275 ARG 0.003 0.000 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 124 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 0.529 Fit side-chains REVERT: A 5 ASP cc_start: 0.8260 (t0) cc_final: 0.7987 (t0) REVERT: A 135 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7318 (mm-40) REVERT: B 51 ILE cc_start: 0.8278 (mp) cc_final: 0.8018 (pt) outliers start: 29 outliers final: 23 residues processed: 114 average time/residue: 0.1468 time to fit residues: 22.1190 Evaluate side-chains 114 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 127 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 237 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 282 ASP 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 383 PHE 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 58 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4919 Z= 0.250 Angle : 0.642 9.384 6690 Z= 0.312 Chirality : 0.041 0.150 763 Planarity : 0.004 0.044 833 Dihedral : 3.948 15.337 675 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.60 % Allowed : 30.29 % Favored : 63.11 % 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: 0.97 (0.36), residues: 612 helix: 1.61 (0.28), residues: 373 sheet: -1.19 (0.81), residues: 47 loop : -0.73 (0.47), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 33 HIS 0.003 0.001 HIS A 47 PHE 0.017 0.002 PHE B 27 TYR 0.015 0.001 TYR A 275 ARG 0.003 0.000 ARG B 67 *********************** 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 127 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 93 time to evaluate : 0.519 Fit side-chains REVERT: A 5 ASP cc_start: 0.8304 (t0) cc_final: 0.8012 (t0) REVERT: A 135 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7330 (mm-40) REVERT: B 51 ILE cc_start: 0.8439 (mp) cc_final: 0.8177 (pt) REVERT: B 60 TYR cc_start: 0.7462 (m-80) cc_final: 0.6754 (m-10) outliers start: 34 outliers final: 26 residues processed: 119 average time/residue: 0.1438 time to fit residues: 22.7619 Evaluate side-chains 116 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 127 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 177 THR Chi-restraints excluded: chain A residue 202 ILE 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 282 ASP 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 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 34 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 8.9990 chunk 53 optimal weight: 0.0020 overall best weight: 1.1192 ------------------------------------------------------------------------------- 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: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4919 Z= 0.264 Angle : 0.658 9.447 6690 Z= 0.317 Chirality : 0.041 0.150 763 Planarity : 0.004 0.044 833 Dihedral : 3.971 14.385 675 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 7.18 % Allowed : 29.51 % 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: 0.97 (0.36), residues: 612 helix: 1.61 (0.28), residues: 373 sheet: -1.20 (0.81), residues: 47 loop : -0.75 (0.46), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 247 HIS 0.003 0.001 HIS B 105 PHE 0.016 0.001 PHE A 351 TYR 0.013 0.001 TYR A 264 ARG 0.003 0.000 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 132 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 0.489 Fit side-chains REVERT: A 5 ASP cc_start: 0.8312 (t0) cc_final: 0.8002 (t0) REVERT: A 135 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7307 (mm-40) REVERT: A 383 PHE cc_start: 0.8552 (t80) cc_final: 0.8317 (m-80) REVERT: B 51 ILE cc_start: 0.8511 (mp) cc_final: 0.8187 (pt) REVERT: B 60 TYR cc_start: 0.7466 (m-80) cc_final: 0.6775 (m-10) outliers start: 37 outliers final: 29 residues processed: 120 average time/residue: 0.1397 time to fit residues: 22.1620 Evaluate side-chains 122 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 127 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 170 LEU 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 256 VAL Chi-restraints excluded: chain A residue 282 ASP 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 399 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.0040 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.6136 ------------------------------------------------------------------------------- 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: 0.7606 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4919 Z= 0.201 Angle : 0.650 9.655 6690 Z= 0.310 Chirality : 0.039 0.154 763 Planarity : 0.004 0.042 833 Dihedral : 3.931 13.632 675 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.99 % Allowed : 30.29 % Favored : 62.72 % 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: 1.73 (0.28), residues: 373 sheet: -1.22 (0.79), residues: 47 loop : -0.69 (0.47), residues: 192 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 0.012 0.001 TYR A 264 ARG 0.006 0.000 ARG A 310 *********************** 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 131 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 0.506 Fit side-chains REVERT: A 5 ASP cc_start: 0.8320 (t0) cc_final: 0.8036 (t0) REVERT: A 135 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7302 (mm-40) REVERT: A 140 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8489 (mt) REVERT: A 310 ARG cc_start: 0.7249 (mtm-85) cc_final: 0.6956 (mtm-85) REVERT: A 383 PHE cc_start: 0.8526 (t80) cc_final: 0.8279 (m-80) REVERT: B 51 ILE cc_start: 0.8450 (mp) cc_final: 0.8135 (pt) REVERT: B 60 TYR cc_start: 0.7421 (m-80) cc_final: 0.7220 (m-10) outliers start: 36 outliers final: 26 residues processed: 119 average time/residue: 0.1301 time to fit residues: 20.6244 Evaluate side-chains 121 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.456 ------------------------------------------------------------------------------- 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 127 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 170 LEU 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 275 TYR Chi-restraints excluded: chain A residue 282 ASP 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 overall best weight: 0.3676 ------------------------------------------------------------------------------- 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: 0.7561 moved from start: 0.1457 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= 0.177 Angle : 0.638 10.807 6690 Z= 0.303 Chirality : 0.039 0.162 763 Planarity : 0.004 0.041 833 Dihedral : 3.855 13.514 675 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.60 % Allowed : 31.07 % Favored : 62.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.36), residues: 612 helix: 1.88 (0.28), residues: 371 sheet: -1.24 (0.78), residues: 47 loop : -0.66 (0.48), residues: 194 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 0.021 0.001 PHE B 27 TYR 0.012 0.001 TYR A 264 ARG 0.006 0.000 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 128 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 94 time to evaluate : 0.551 Fit side-chains REVERT: A 5 ASP cc_start: 0.8294 (t0) cc_final: 0.8029 (t0) REVERT: A 135 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7281 (mm-40) outliers start: 34 outliers final: 27 residues processed: 117 average time/residue: 0.1414 time to fit residues: 22.4053 Evaluate side-chains 121 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 93 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 127 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 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 275 TYR Chi-restraints excluded: chain A residue 282 ASP 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 chunk 54 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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: 0.7592 moved from start: 0.1490 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= 0.205 Angle : 0.643 10.035 6690 Z= 0.307 Chirality : 0.040 0.167 763 Planarity : 0.004 0.041 833 Dihedral : 3.822 13.432 675 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.02 % Allowed : 31.46 % Favored : 62.52 % 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: 1.24 (0.36), residues: 612 helix: 1.88 (0.28), residues: 371 sheet: -1.35 (0.78), residues: 47 loop : -0.64 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 33 HIS 0.003 0.001 HIS A 34 PHE 0.014 0.001 PHE A 351 TYR 0.012 0.001 TYR A 264 ARG 0.007 0.000 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 123 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 92 time to evaluate : 0.527 Fit side-chains REVERT: A 5 ASP cc_start: 0.8308 (t0) cc_final: 0.8036 (t0) REVERT: A 135 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7306 (mm-40) REVERT: A 140 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8501 (mt) REVERT: B 60 TYR cc_start: 0.7209 (m-80) cc_final: 0.6822 (m-10) outliers start: 31 outliers final: 26 residues processed: 112 average time/residue: 0.1262 time to fit residues: 19.2588 Evaluate side-chains 119 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 127 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 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 275 TYR Chi-restraints excluded: chain A residue 282 ASP 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 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 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: 0.9990 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 0.0370 chunk 54 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- 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: 0.7592 moved from start: 0.1576 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= 0.204 Angle : 0.646 11.867 6690 Z= 0.308 Chirality : 0.040 0.171 763 Planarity : 0.004 0.042 833 Dihedral : 3.816 13.229 675 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 6.02 % Allowed : 31.84 % Favored : 62.14 % 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 (0.36), residues: 612 helix: 1.87 (0.28), residues: 371 sheet: -1.38 (0.78), residues: 47 loop : -0.68 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 47 HIS 0.003 0.001 HIS A 34 PHE 0.023 0.001 PHE B 27 TYR 0.012 0.001 TYR A 264 ARG 0.007 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 122 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 91 time to evaluate : 0.543 Fit side-chains REVERT: A 5 ASP cc_start: 0.8302 (t0) cc_final: 0.8036 (t0) REVERT: A 135 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7305 (mm-40) REVERT: A 140 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8487 (mt) REVERT: B 60 TYR cc_start: 0.7187 (m-80) cc_final: 0.6815 (m-10) outliers start: 31 outliers final: 27 residues processed: 111 average time/residue: 0.1235 time to fit residues: 19.0597 Evaluate side-chains 119 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 90 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 127 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 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 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASP 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 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 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: 7.9990 chunk 48 optimal weight: 0.0870 chunk 5 optimal weight: 0.0040 chunk 37 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.4970 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.1589 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= 0.186 Angle : 0.638 11.693 6690 Z= 0.303 Chirality : 0.039 0.169 763 Planarity : 0.004 0.041 833 Dihedral : 3.790 13.222 675 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 5.24 % Allowed : 32.62 % Favored : 62.14 % 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: 1.29 (0.36), residues: 612 helix: 1.92 (0.28), residues: 371 sheet: -1.40 (0.78), residues: 47 loop : -0.61 (0.48), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 33 HIS 0.003 0.001 HIS A 34 PHE 0.013 0.001 PHE B 68 TYR 0.011 0.001 TYR A 264 ARG 0.007 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 122 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 95 time to evaluate : 0.534 Fit side-chains REVERT: A 5 ASP cc_start: 0.8328 (t0) cc_final: 0.8091 (t0) REVERT: A 135 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7297 (mm-40) REVERT: A 140 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8481 (mt) REVERT: B 60 TYR cc_start: 0.7184 (m-80) cc_final: 0.6844 (m-10) outliers start: 27 outliers final: 25 residues processed: 113 average time/residue: 0.1353 time to fit residues: 20.5542 Evaluate side-chains 117 residues out of total 513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 90 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 127 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 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 256 VAL Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 275 TYR Chi-restraints excluded: chain A residue 282 ASP 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 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 111 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1571 > 50: distance: 11 - 17: 3.027 distance: 27 - 47: 7.141 distance: 33 - 58: 11.140 distance: 38 - 62: 9.014 distance: 41 - 47: 6.200 distance: 42 - 67: 13.840 distance: 47 - 48: 4.150 distance: 48 - 49: 10.979 distance: 48 - 51: 4.979 distance: 49 - 50: 7.901 distance: 49 - 58: 14.503 distance: 50 - 74: 15.612 distance: 51 - 52: 7.671 distance: 52 - 53: 5.792 distance: 52 - 54: 10.256 distance: 53 - 55: 7.378 distance: 54 - 56: 10.088 distance: 55 - 57: 10.496 distance: 56 - 57: 11.822 distance: 58 - 59: 11.335 distance: 59 - 60: 10.053 distance: 60 - 61: 9.403 distance: 60 - 62: 4.931 distance: 62 - 63: 6.384 distance: 63 - 64: 21.656 distance: 63 - 66: 15.054 distance: 64 - 65: 26.345 distance: 64 - 67: 8.103 distance: 67 - 68: 9.002 distance: 68 - 69: 10.859 distance: 68 - 71: 21.252 distance: 69 - 70: 16.492 distance: 69 - 74: 17.101 distance: 71 - 72: 19.040 distance: 71 - 73: 18.726 distance: 74 - 75: 14.398 distance: 75 - 76: 23.707 distance: 75 - 78: 28.351 distance: 76 - 77: 13.395 distance: 76 - 82: 58.637 distance: 78 - 79: 19.027 distance: 79 - 80: 35.847 distance: 79 - 81: 22.910 distance: 82 - 83: 40.759 distance: 83 - 84: 35.905 distance: 83 - 86: 37.861 distance: 84 - 85: 25.958 distance: 84 - 90: 14.574 distance: 85 - 111: 25.188 distance: 86 - 87: 23.200 distance: 87 - 88: 7.784 distance: 87 - 89: 24.508 distance: 90 - 91: 16.468 distance: 90 - 96: 19.635 distance: 91 - 92: 28.366 distance: 91 - 94: 18.542 distance: 92 - 93: 24.736 distance: 92 - 97: 36.224 distance: 93 - 122: 10.377 distance: 94 - 95: 10.338 distance: 95 - 96: 17.418 distance: 97 - 98: 17.958 distance: 98 - 99: 5.407 distance: 98 - 101: 17.662 distance: 99 - 100: 6.269 distance: 99 - 102: 18.878 distance: 100 - 129: 11.654 distance: 102 - 103: 14.646 distance: 103 - 104: 16.660 distance: 103 - 106: 16.902 distance: 104 - 105: 19.531 distance: 104 - 111: 9.083 distance: 105 - 134: 12.789 distance: 106 - 107: 18.659 distance: 107 - 108: 14.391 distance: 108 - 109: 17.982 distance: 109 - 110: 12.396 distance: 112 - 115: 3.515 distance: 113 - 114: 6.705 distance: 114 - 141: 8.039 distance: 115 - 116: 4.936 distance: 116 - 117: 4.132 distance: 116 - 118: 6.572 distance: 117 - 119: 3.111 distance: 118 - 120: 4.262 distance: 119 - 121: 4.496 distance: 120 - 121: 3.229