Starting phenix.real_space_refine on Mon Sep 23 22:19:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/09_2024/8ej5_28176.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/09_2024/8ej5_28176.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/09_2024/8ej5_28176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/09_2024/8ej5_28176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/09_2024/8ej5_28176.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ej5_28176/09_2024/8ej5_28176.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 3712 2.51 5 N 981 2.21 5 O 1108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5818 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3556 Classifications: {'peptide': 457} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "C" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 754 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 88} Time building chain proxies: 3.92, per 1000 atoms: 0.67 Number of scatterers: 5818 At special positions: 0 Unit cell: (74.368, 95.616, 131.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 1108 8.00 N 981 7.00 C 3712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.41 Conformation dependent library (CDL) restraints added in 676.3 milliseconds 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1328 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 2 sheets defined 59.3% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 22 through 30 removed outlier: 4.300A pdb=" N GLY A 28 " --> pdb=" O ASP A 24 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 43 through 58 Processing helix chain 'A' and resid 60 through 72 Processing helix chain 'A' and resid 88 through 106 Processing helix chain 'A' and resid 123 through 137 Processing helix chain 'A' and resid 142 through 148 Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.151A pdb=" N TRP A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.513A pdb=" N LEU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 353 through 367 Processing helix chain 'A' and resid 382 through 390 removed outlier: 3.662A pdb=" N VAL A 386 " --> pdb=" O ARG A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 464 No H-bonds generated for 'chain 'A' and resid 462 through 464' Processing helix chain 'B' and resid 2 through 21 removed outlier: 3.824A pdb=" N GLN B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 45 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 61 through 68 removed outlier: 3.529A pdb=" N TYR B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 86 Processing helix chain 'C' and resid 2 through 21 removed outlier: 3.825A pdb=" N GLN C 21 " --> pdb=" O ASN C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 45 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 61 through 68 removed outlier: 3.526A pdb=" N TYR C 65 " --> pdb=" O SER C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 86 Processing helix chain 'D' and resid 2 through 21 removed outlier: 3.806A pdb=" N GLN D 21 " --> pdb=" O ASN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 45 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 61 through 68 removed outlier: 3.527A pdb=" N TYR D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 86 Processing sheet with id=AA1, first strand: chain 'A' and resid 249 through 255 removed outlier: 6.199A pdb=" N THR A 258 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 312 through 317 removed outlier: 5.139A pdb=" N GLY A 315 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 454 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 434 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLY A 422 " --> pdb=" O PHE A 404 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 906 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: 1.35 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1171 1.32 - 1.45: 1552 1.45 - 1.57: 3214 1.57 - 1.70: 0 1.70 - 1.82: 29 Bond restraints: 5966 Sorted by residual: bond pdb=" N VAL A 394 " pdb=" CA VAL A 394 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.29e+01 bond pdb=" N VAL A 440 " pdb=" CA VAL A 440 " ideal model delta sigma weight residual 1.462 1.492 -0.031 8.70e-03 1.32e+04 1.23e+01 bond pdb=" N VAL A 425 " pdb=" CA VAL A 425 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.22e+01 bond pdb=" N VAL A 427 " pdb=" CA VAL A 427 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.14e-02 7.69e+03 1.22e+01 bond pdb=" N GLU D 47 " pdb=" CA GLU D 47 " ideal model delta sigma weight residual 1.461 1.491 -0.030 9.20e-03 1.18e+04 1.07e+01 ... (remaining 5961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 6245 1.82 - 3.65: 1697 3.65 - 5.47: 133 5.47 - 7.29: 23 7.29 - 9.12: 2 Bond angle restraints: 8100 Sorted by residual: angle pdb=" CA GLY A 314 " pdb=" C GLY A 314 " pdb=" N GLY A 315 " ideal model delta sigma weight residual 115.11 120.97 -5.86 9.50e-01 1.11e+00 3.81e+01 angle pdb=" N GLY A 315 " pdb=" CA GLY A 315 " pdb=" C GLY A 315 " ideal model delta sigma weight residual 110.56 118.63 -8.07 1.36e+00 5.41e-01 3.52e+01 angle pdb=" N ASN A 284 " pdb=" CA ASN A 284 " pdb=" C ASN A 284 " ideal model delta sigma weight residual 111.54 104.26 7.28 1.36e+00 5.41e-01 2.87e+01 angle pdb=" N LYS A 272 " pdb=" CA LYS A 272 " pdb=" C LYS A 272 " ideal model delta sigma weight residual 111.28 105.48 5.80 1.09e+00 8.42e-01 2.83e+01 angle pdb=" CA LYS A 242 " pdb=" C LYS A 242 " pdb=" O LYS A 242 " ideal model delta sigma weight residual 120.63 114.92 5.71 1.08e+00 8.57e-01 2.80e+01 ... (remaining 8095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.49: 3161 16.49 - 32.97: 214 32.97 - 49.46: 63 49.46 - 65.95: 11 65.95 - 82.44: 3 Dihedral angle restraints: 3452 sinusoidal: 1360 harmonic: 2092 Sorted by residual: dihedral pdb=" C ASN A 316 " pdb=" N ASN A 316 " pdb=" CA ASN A 316 " pdb=" CB ASN A 316 " ideal model delta harmonic sigma weight residual -122.60 -133.15 10.55 0 2.50e+00 1.60e-01 1.78e+01 dihedral pdb=" N ASN A 465 " pdb=" CA ASN A 465 " pdb=" CB ASN A 465 " pdb=" CG ASN A 465 " ideal model delta sinusoidal sigma weight residual -180.00 -125.56 -54.44 3 1.50e+01 4.44e-03 9.28e+00 dihedral pdb=" CA ILE A 275 " pdb=" CB ILE A 275 " pdb=" CG1 ILE A 275 " pdb=" CD1 ILE A 275 " ideal model delta sinusoidal sigma weight residual -180.00 -127.13 -52.87 3 1.50e+01 4.44e-03 9.15e+00 ... (remaining 3449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 366 0.067 - 0.135: 376 0.135 - 0.202: 85 0.202 - 0.270: 6 0.270 - 0.337: 2 Chirality restraints: 835 Sorted by residual: chirality pdb=" CA ILE A 251 " pdb=" N ILE A 251 " pdb=" C ILE A 251 " pdb=" CB ILE A 251 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA ILE A 238 " pdb=" N ILE A 238 " pdb=" C ILE A 238 " pdb=" CB ILE A 238 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASN A 316 " pdb=" N ASN A 316 " pdb=" C ASN A 316 " pdb=" CB ASN A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 832 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 84 " -0.019 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C SER A 84 " 0.064 2.00e-02 2.50e+03 pdb=" O SER A 84 " -0.023 2.00e-02 2.50e+03 pdb=" N PRO A 85 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 78 " 0.045 2.00e-02 2.50e+03 2.29e-02 1.05e+01 pdb=" CG TYR D 78 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR D 78 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR D 78 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR D 78 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 78 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR D 78 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 78 " 0.042 2.00e-02 2.50e+03 2.19e-02 9.62e+00 pdb=" CG TYR B 78 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 78 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 78 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 78 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 78 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 78 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 78 " 0.019 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 2740 2.96 - 3.44: 6379 3.44 - 3.93: 10549 3.93 - 4.41: 11549 4.41 - 4.90: 18520 Nonbonded interactions: 49737 Sorted by model distance: nonbonded pdb=" O SER A 84 " pdb=" OE1 GLU B 58 " model vdw 2.472 3.040 nonbonded pdb=" O ARG A 311 " pdb=" N ASP A 456 " model vdw 2.478 3.120 nonbonded pdb=" N PHE A 244 " pdb=" O ILE A 251 " model vdw 2.487 3.120 nonbonded pdb=" O GLY A 281 " pdb=" OD1 ASP A 464 " model vdw 2.488 3.040 nonbonded pdb=" N THR A 318 " pdb=" OD1 ASN A 321 " model vdw 2.490 3.120 ... (remaining 49732 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.670 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 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 : 0.012 0.047 5966 Z= 0.776 Angle : 1.519 9.118 8100 Z= 1.153 Chirality : 0.090 0.337 835 Planarity : 0.010 0.109 1071 Dihedral : 12.691 82.437 2124 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.84 % Allowed : 1.95 % Favored : 97.21 % Rotamer: Outliers : 3.27 % Allowed : 4.91 % Favored : 91.82 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.30), residues: 717 helix: 1.44 (0.25), residues: 397 sheet: 0.11 (0.71), residues: 42 loop : 0.49 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.006 TRP A 79 HIS 0.019 0.004 HIS C 88 PHE 0.024 0.004 PHE B 77 TYR 0.045 0.005 TYR D 78 ARG 0.008 0.002 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 328 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7439 (ttm) cc_final: 0.6453 (ttm) REVERT: A 33 ILE cc_start: 0.6295 (mt) cc_final: 0.6059 (mt) REVERT: A 74 ASN cc_start: 0.6556 (t0) cc_final: 0.4873 (t0) REVERT: A 80 LEU cc_start: 0.8388 (tp) cc_final: 0.8181 (tp) REVERT: A 176 ASN cc_start: 0.9194 (t0) cc_final: 0.8478 (p0) REVERT: A 179 LEU cc_start: 0.8689 (tp) cc_final: 0.7989 (tp) REVERT: A 229 ASP cc_start: 0.8564 (m-30) cc_final: 0.8296 (m-30) REVERT: A 234 ASP cc_start: 0.8173 (m-30) cc_final: 0.7842 (t0) REVERT: A 241 ASP cc_start: 0.8580 (m-30) cc_final: 0.8082 (p0) REVERT: A 322 LEU cc_start: 0.8657 (tp) cc_final: 0.8281 (tp) REVERT: A 335 PHE cc_start: 0.7934 (t80) cc_final: 0.7420 (t80) REVERT: A 350 ASP cc_start: 0.8412 (m-30) cc_final: 0.7843 (m-30) REVERT: A 357 LEU cc_start: 0.9093 (tp) cc_final: 0.8798 (tp) REVERT: A 361 TYR cc_start: 0.8506 (t80) cc_final: 0.8182 (t80) REVERT: A 362 MET cc_start: 0.9093 (mmm) cc_final: 0.8638 (mmt) REVERT: A 363 HIS cc_start: 0.8420 (t-170) cc_final: 0.8072 (t70) REVERT: A 366 TRP cc_start: 0.7592 (m100) cc_final: 0.7165 (m100) REVERT: A 412 GLN cc_start: 0.8505 (mt0) cc_final: 0.8260 (mt0) REVERT: A 438 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6783 (m-10) REVERT: A 439 ASN cc_start: 0.8977 (t0) cc_final: 0.8442 (t0) REVERT: A 455 ILE cc_start: 0.8795 (mm) cc_final: 0.8249 (mp) REVERT: A 469 PHE cc_start: 0.8974 (p90) cc_final: 0.8695 (p90) REVERT: B 19 LEU cc_start: 0.8990 (mt) cc_final: 0.8728 (mt) REVERT: B 89 ILE cc_start: 0.5995 (pt) cc_final: 0.5415 (pt) REVERT: C 12 MET cc_start: 0.8845 (tpt) cc_final: 0.8053 (tpt) REVERT: C 19 LEU cc_start: 0.9480 (mt) cc_final: 0.9270 (mt) REVERT: C 36 VAL cc_start: 0.9385 (t) cc_final: 0.9032 (m) REVERT: C 38 CYS cc_start: 0.9134 (m) cc_final: 0.7947 (t) REVERT: C 42 LEU cc_start: 0.8909 (mt) cc_final: 0.6001 (mt) REVERT: C 62 LEU cc_start: 0.9434 (tp) cc_final: 0.9090 (tp) REVERT: C 77 PHE cc_start: 0.8051 (t80) cc_final: 0.7832 (t80) REVERT: C 82 TYR cc_start: 0.8394 (t80) cc_final: 0.7898 (t80) REVERT: D 15 LEU cc_start: 0.9449 (tp) cc_final: 0.9114 (tp) REVERT: D 17 ASN cc_start: 0.8021 (m-40) cc_final: 0.7456 (m110) REVERT: D 19 LEU cc_start: 0.9459 (mt) cc_final: 0.9172 (mt) REVERT: D 66 LEU cc_start: 0.8729 (mt) cc_final: 0.8485 (mt) REVERT: D 74 GLN cc_start: 0.8940 (mt0) cc_final: 0.8290 (mm-40) outliers start: 20 outliers final: 5 residues processed: 333 average time/residue: 0.1877 time to fit residues: 78.6431 Evaluate side-chains 197 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 56 optimal weight: 0.2980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS C 32 ASN D 33 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6854 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5966 Z= 0.184 Angle : 0.645 9.858 8100 Z= 0.342 Chirality : 0.044 0.258 835 Planarity : 0.006 0.143 1071 Dihedral : 5.728 87.919 784 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 1.81 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.70 (0.32), residues: 717 helix: 1.82 (0.26), residues: 403 sheet: 0.43 (0.75), residues: 44 loop : 0.30 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 156 HIS 0.004 0.001 HIS A 396 PHE 0.023 0.003 PHE D 25 TYR 0.019 0.002 TYR D 78 ARG 0.008 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ASP cc_start: 0.6962 (t0) cc_final: 0.6411 (t0) REVERT: A 137 ASN cc_start: 0.7624 (t0) cc_final: 0.7261 (t0) REVERT: A 176 ASN cc_start: 0.9177 (t0) cc_final: 0.8388 (p0) REVERT: A 179 LEU cc_start: 0.8647 (tp) cc_final: 0.7750 (tt) REVERT: A 248 MET cc_start: 0.9223 (mpp) cc_final: 0.8743 (mpp) REVERT: A 278 ILE cc_start: 0.8435 (mp) cc_final: 0.7958 (tt) REVERT: A 330 ILE cc_start: 0.7948 (mt) cc_final: 0.7580 (mt) REVERT: A 383 VAL cc_start: 0.9541 (p) cc_final: 0.9289 (p) REVERT: A 394 VAL cc_start: 0.8126 (t) cc_final: 0.7866 (t) REVERT: A 439 ASN cc_start: 0.9254 (t0) cc_final: 0.8309 (t0) REVERT: A 467 MET cc_start: 0.6743 (tpp) cc_final: 0.6474 (tpp) REVERT: A 468 PHE cc_start: 0.7967 (m-80) cc_final: 0.7691 (m-80) REVERT: B 19 LEU cc_start: 0.8560 (mt) cc_final: 0.8162 (mt) REVERT: B 88 HIS cc_start: 0.3842 (m170) cc_final: 0.3471 (m-70) REVERT: C 4 GLU cc_start: 0.8043 (mp0) cc_final: 0.7682 (tm-30) REVERT: C 9 TYR cc_start: 0.7878 (m-10) cc_final: 0.7507 (m-10) REVERT: C 12 MET cc_start: 0.8863 (tpt) cc_final: 0.8423 (ptt) REVERT: C 16 PHE cc_start: 0.9241 (t80) cc_final: 0.8994 (t80) REVERT: C 27 THR cc_start: 0.8369 (m) cc_final: 0.8137 (m) REVERT: C 52 PHE cc_start: 0.9010 (t80) cc_final: 0.8601 (t80) REVERT: C 55 ASP cc_start: 0.7904 (t70) cc_final: 0.7464 (t0) REVERT: C 62 LEU cc_start: 0.9449 (tp) cc_final: 0.9232 (tp) REVERT: C 82 TYR cc_start: 0.8651 (t80) cc_final: 0.7801 (t80) REVERT: D 15 LEU cc_start: 0.9303 (tp) cc_final: 0.8996 (tp) REVERT: D 18 LEU cc_start: 0.9607 (mm) cc_final: 0.9363 (mm) REVERT: D 19 LEU cc_start: 0.9240 (mt) cc_final: 0.8864 (mt) REVERT: D 33 ASN cc_start: 0.8809 (m110) cc_final: 0.8391 (m-40) REVERT: D 55 ASP cc_start: 0.8079 (t0) cc_final: 0.7691 (t0) REVERT: D 59 ASP cc_start: 0.9285 (m-30) cc_final: 0.8957 (m-30) REVERT: D 63 LEU cc_start: 0.9484 (mt) cc_final: 0.9220 (mp) REVERT: D 66 LEU cc_start: 0.9039 (mt) cc_final: 0.8809 (mt) REVERT: D 74 GLN cc_start: 0.8968 (mt0) cc_final: 0.8106 (mm110) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1526 time to fit residues: 49.3332 Evaluate side-chains 187 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 20 GLN ** D 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5966 Z= 0.178 Angle : 0.603 9.581 8100 Z= 0.317 Chirality : 0.042 0.196 835 Planarity : 0.004 0.044 1071 Dihedral : 5.254 62.817 784 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.09 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 1.36 (0.32), residues: 717 helix: 1.53 (0.26), residues: 402 sheet: 0.12 (0.73), residues: 50 loop : 0.24 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 75 HIS 0.004 0.001 HIS A 363 PHE 0.020 0.002 PHE C 25 TYR 0.021 0.002 TYR B 9 ARG 0.008 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 137 ASN cc_start: 0.7637 (t0) cc_final: 0.7030 (t0) REVERT: A 174 TYR cc_start: 0.6921 (m-10) cc_final: 0.6592 (m-80) REVERT: A 176 ASN cc_start: 0.9148 (t0) cc_final: 0.8498 (p0) REVERT: A 251 ILE cc_start: 0.9236 (mt) cc_final: 0.9000 (mt) REVERT: A 263 MET cc_start: 0.7130 (mtp) cc_final: 0.6762 (mtp) REVERT: A 267 LEU cc_start: 0.9301 (tp) cc_final: 0.9079 (tp) REVERT: A 270 GLU cc_start: 0.8133 (tp30) cc_final: 0.7829 (tp30) REVERT: A 278 ILE cc_start: 0.8816 (mp) cc_final: 0.8591 (mm) REVERT: A 322 LEU cc_start: 0.8689 (tp) cc_final: 0.8359 (tp) REVERT: A 330 ILE cc_start: 0.8092 (mt) cc_final: 0.7767 (mt) REVERT: A 357 LEU cc_start: 0.9019 (tp) cc_final: 0.8752 (tp) REVERT: A 384 TRP cc_start: 0.9310 (p-90) cc_final: 0.8358 (p-90) REVERT: A 412 GLN cc_start: 0.9149 (mt0) cc_final: 0.8902 (mt0) REVERT: A 433 PHE cc_start: 0.8894 (p90) cc_final: 0.8653 (p90) REVERT: A 439 ASN cc_start: 0.9358 (t0) cc_final: 0.8334 (t0) REVERT: A 464 ASP cc_start: 0.7535 (p0) cc_final: 0.7137 (p0) REVERT: A 469 PHE cc_start: 0.8728 (p90) cc_final: 0.8512 (p90) REVERT: B 19 LEU cc_start: 0.8180 (mt) cc_final: 0.7889 (mt) REVERT: B 24 ASP cc_start: 0.7377 (t0) cc_final: 0.6535 (t0) REVERT: B 75 TRP cc_start: 0.8625 (t-100) cc_final: 0.8147 (t-100) REVERT: C 4 GLU cc_start: 0.8682 (mp0) cc_final: 0.7922 (tm-30) REVERT: C 16 PHE cc_start: 0.9323 (t80) cc_final: 0.9046 (t80) REVERT: C 18 LEU cc_start: 0.9347 (mm) cc_final: 0.9087 (mm) REVERT: C 19 LEU cc_start: 0.9257 (mt) cc_final: 0.8973 (mt) REVERT: C 27 THR cc_start: 0.8619 (m) cc_final: 0.7992 (m) REVERT: C 46 ASN cc_start: 0.8253 (p0) cc_final: 0.8019 (p0) REVERT: C 55 ASP cc_start: 0.7875 (t70) cc_final: 0.7599 (t0) REVERT: C 57 ASN cc_start: 0.8617 (t0) cc_final: 0.8413 (t0) REVERT: C 82 TYR cc_start: 0.8964 (t80) cc_final: 0.8704 (t80) REVERT: D 15 LEU cc_start: 0.9402 (tp) cc_final: 0.9162 (tp) REVERT: D 18 LEU cc_start: 0.9566 (mm) cc_final: 0.9320 (mm) REVERT: D 33 ASN cc_start: 0.8778 (m110) cc_final: 0.8388 (m110) REVERT: D 59 ASP cc_start: 0.9345 (m-30) cc_final: 0.9078 (m-30) REVERT: D 63 LEU cc_start: 0.9573 (mt) cc_final: 0.9330 (mt) REVERT: D 66 LEU cc_start: 0.9424 (mt) cc_final: 0.9088 (mt) REVERT: D 70 ASP cc_start: 0.8300 (t70) cc_final: 0.7390 (t0) REVERT: D 74 GLN cc_start: 0.8978 (mt0) cc_final: 0.8195 (mm-40) REVERT: D 89 ILE cc_start: 0.8708 (pt) cc_final: 0.8154 (pt) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1564 time to fit residues: 47.4386 Evaluate side-chains 175 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS B 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5966 Z= 0.174 Angle : 0.603 9.121 8100 Z= 0.314 Chirality : 0.041 0.190 835 Planarity : 0.003 0.031 1071 Dihedral : 5.760 82.720 784 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.09 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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 (0.32), residues: 717 helix: 1.27 (0.26), residues: 407 sheet: -0.05 (0.69), residues: 50 loop : 0.21 (0.41), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 156 HIS 0.005 0.001 HIS A 236 PHE 0.017 0.002 PHE C 77 TYR 0.011 0.001 TYR D 78 ARG 0.004 0.001 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7771 (m-80) cc_final: 0.7482 (m-80) REVERT: A 92 ASP cc_start: 0.7029 (t0) cc_final: 0.6685 (t0) REVERT: A 103 GLN cc_start: 0.7835 (tp40) cc_final: 0.7420 (tp40) REVERT: A 137 ASN cc_start: 0.7835 (t0) cc_final: 0.7026 (t0) REVERT: A 138 MET cc_start: 0.7142 (mmp) cc_final: 0.6855 (mmm) REVERT: A 176 ASN cc_start: 0.9182 (t0) cc_final: 0.8501 (p0) REVERT: A 322 LEU cc_start: 0.8671 (tp) cc_final: 0.8357 (tp) REVERT: A 357 LEU cc_start: 0.9045 (tp) cc_final: 0.8671 (tp) REVERT: A 412 GLN cc_start: 0.9185 (mt0) cc_final: 0.8872 (mt0) REVERT: A 437 ASN cc_start: 0.8777 (p0) cc_final: 0.7412 (p0) REVERT: A 439 ASN cc_start: 0.9305 (t0) cc_final: 0.8292 (t0) REVERT: A 451 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7433 (mt-10) REVERT: A 467 MET cc_start: 0.7957 (ttm) cc_final: 0.7703 (ttm) REVERT: B 19 LEU cc_start: 0.8239 (mt) cc_final: 0.7557 (mt) REVERT: B 20 GLN cc_start: 0.6707 (tp40) cc_final: 0.5352 (tp-100) REVERT: B 24 ASP cc_start: 0.7388 (t0) cc_final: 0.6182 (t0) REVERT: B 89 ILE cc_start: 0.6199 (pt) cc_final: 0.5864 (pt) REVERT: C 4 GLU cc_start: 0.8669 (mp0) cc_final: 0.7944 (tm-30) REVERT: C 16 PHE cc_start: 0.9355 (t80) cc_final: 0.8858 (t80) REVERT: C 20 GLN cc_start: 0.8779 (mt0) cc_final: 0.8399 (mt0) REVERT: C 27 THR cc_start: 0.8682 (m) cc_final: 0.8043 (m) REVERT: C 41 LEU cc_start: 0.9457 (mt) cc_final: 0.9192 (mt) REVERT: C 42 LEU cc_start: 0.8807 (mt) cc_final: 0.8525 (mt) REVERT: C 46 ASN cc_start: 0.8221 (p0) cc_final: 0.7962 (p0) REVERT: C 55 ASP cc_start: 0.7911 (t70) cc_final: 0.7538 (t0) REVERT: D 18 LEU cc_start: 0.9608 (mm) cc_final: 0.9309 (mm) REVERT: D 33 ASN cc_start: 0.8880 (m110) cc_final: 0.8443 (m110) REVERT: D 52 PHE cc_start: 0.9300 (t80) cc_final: 0.9010 (t80) REVERT: D 55 ASP cc_start: 0.8258 (t0) cc_final: 0.7653 (t0) REVERT: D 66 LEU cc_start: 0.9526 (mt) cc_final: 0.9213 (mt) REVERT: D 89 ILE cc_start: 0.8806 (pt) cc_final: 0.8374 (pt) outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1536 time to fit residues: 47.7020 Evaluate side-chains 180 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 0.0470 chunk 51 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 17 optimal weight: 8.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 461 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.7687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5966 Z= 0.290 Angle : 0.720 9.748 8100 Z= 0.376 Chirality : 0.044 0.184 835 Planarity : 0.004 0.037 1071 Dihedral : 6.187 78.020 784 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.93 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.66 (0.31), residues: 717 helix: 0.93 (0.26), residues: 407 sheet: -0.29 (0.70), residues: 50 loop : -0.02 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 156 HIS 0.008 0.002 HIS A 363 PHE 0.021 0.002 PHE D 25 TYR 0.018 0.002 TYR A 438 ARG 0.004 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8024 (m-80) cc_final: 0.7671 (m-80) REVERT: A 77 TRP cc_start: 0.7317 (m-90) cc_final: 0.6960 (m-90) REVERT: A 92 ASP cc_start: 0.6874 (t0) cc_final: 0.6217 (t0) REVERT: A 137 ASN cc_start: 0.7752 (t0) cc_final: 0.6855 (t0) REVERT: A 176 ASN cc_start: 0.9256 (t0) cc_final: 0.8455 (p0) REVERT: A 270 GLU cc_start: 0.7805 (tp30) cc_final: 0.7546 (tp30) REVERT: A 322 LEU cc_start: 0.8713 (tp) cc_final: 0.8379 (tp) REVERT: A 357 LEU cc_start: 0.9217 (tp) cc_final: 0.8876 (tp) REVERT: A 412 GLN cc_start: 0.9270 (mt0) cc_final: 0.8927 (mt0) REVERT: A 435 THR cc_start: 0.8864 (p) cc_final: 0.8603 (p) REVERT: A 437 ASN cc_start: 0.8681 (p0) cc_final: 0.7545 (p0) REVERT: A 439 ASN cc_start: 0.9392 (t0) cc_final: 0.8344 (t0) REVERT: A 451 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7429 (mt-10) REVERT: A 467 MET cc_start: 0.8322 (ttm) cc_final: 0.7923 (ttm) REVERT: B 19 LEU cc_start: 0.8519 (mt) cc_final: 0.8081 (mt) REVERT: B 24 ASP cc_start: 0.6964 (t0) cc_final: 0.6102 (t0) REVERT: B 34 LEU cc_start: 0.8795 (tp) cc_final: 0.8577 (tp) REVERT: C 4 GLU cc_start: 0.8605 (mp0) cc_final: 0.7999 (tm-30) REVERT: C 9 TYR cc_start: 0.8158 (m-10) cc_final: 0.7901 (m-80) REVERT: C 10 THR cc_start: 0.9347 (m) cc_final: 0.9133 (p) REVERT: C 16 PHE cc_start: 0.9523 (t80) cc_final: 0.9199 (t80) REVERT: C 27 THR cc_start: 0.8757 (m) cc_final: 0.7630 (m) REVERT: C 41 LEU cc_start: 0.9569 (mt) cc_final: 0.9334 (mt) REVERT: C 46 ASN cc_start: 0.8449 (p0) cc_final: 0.8220 (m-40) REVERT: C 55 ASP cc_start: 0.8194 (t70) cc_final: 0.7802 (t0) REVERT: C 78 TYR cc_start: 0.8413 (t80) cc_final: 0.8002 (t80) REVERT: C 79 LYS cc_start: 0.8305 (ptpp) cc_final: 0.7753 (pttm) REVERT: D 15 LEU cc_start: 0.9446 (tp) cc_final: 0.9223 (tp) REVERT: D 19 LEU cc_start: 0.9228 (mt) cc_final: 0.8935 (mt) REVERT: D 55 ASP cc_start: 0.8063 (t0) cc_final: 0.7651 (t0) REVERT: D 63 LEU cc_start: 0.9734 (mt) cc_final: 0.9405 (mt) REVERT: D 66 LEU cc_start: 0.9452 (mt) cc_final: 0.9171 (mt) REVERT: D 74 GLN cc_start: 0.9097 (mt0) cc_final: 0.8280 (mm-40) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1584 time to fit residues: 45.7648 Evaluate side-chains 178 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.0870 chunk 36 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 HIS B 14 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 GLN ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.7889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5966 Z= 0.183 Angle : 0.633 7.900 8100 Z= 0.331 Chirality : 0.042 0.185 835 Planarity : 0.003 0.034 1071 Dihedral : 5.951 77.675 784 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.21 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.69 (0.31), residues: 717 helix: 1.02 (0.26), residues: 401 sheet: 0.27 (0.74), residues: 46 loop : -0.22 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 22 HIS 0.005 0.001 HIS A 236 PHE 0.011 0.001 PHE D 77 TYR 0.027 0.002 TYR D 9 ARG 0.003 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8019 (m-80) cc_final: 0.7698 (m-80) REVERT: A 77 TRP cc_start: 0.6944 (m-90) cc_final: 0.6657 (m-90) REVERT: A 92 ASP cc_start: 0.6990 (t0) cc_final: 0.6053 (t0) REVERT: A 100 LEU cc_start: 0.9108 (mm) cc_final: 0.8900 (mm) REVERT: A 137 ASN cc_start: 0.7816 (t0) cc_final: 0.6896 (t0) REVERT: A 176 ASN cc_start: 0.9194 (t0) cc_final: 0.8301 (p0) REVERT: A 244 PHE cc_start: 0.8306 (m-10) cc_final: 0.8064 (m-10) REVERT: A 270 GLU cc_start: 0.7740 (tp30) cc_final: 0.7088 (tp30) REVERT: A 271 MET cc_start: 0.8532 (mmp) cc_final: 0.7993 (mmm) REVERT: A 273 ASP cc_start: 0.8312 (m-30) cc_final: 0.8092 (m-30) REVERT: A 322 LEU cc_start: 0.8634 (tp) cc_final: 0.8346 (tp) REVERT: A 357 LEU cc_start: 0.9178 (tp) cc_final: 0.8693 (tp) REVERT: A 437 ASN cc_start: 0.8891 (p0) cc_final: 0.7909 (p0) REVERT: A 439 ASN cc_start: 0.9319 (t0) cc_final: 0.8303 (t0) REVERT: A 451 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 467 MET cc_start: 0.8386 (ttm) cc_final: 0.8053 (ttm) REVERT: B 19 LEU cc_start: 0.8222 (mt) cc_final: 0.7888 (mt) REVERT: B 24 ASP cc_start: 0.7094 (t0) cc_final: 0.6278 (t0) REVERT: B 89 ILE cc_start: 0.7043 (pt) cc_final: 0.6257 (pt) REVERT: C 16 PHE cc_start: 0.9539 (t80) cc_final: 0.9137 (t80) REVERT: C 24 ASP cc_start: 0.8034 (t0) cc_final: 0.7511 (t0) REVERT: C 41 LEU cc_start: 0.9540 (mt) cc_final: 0.9292 (mt) REVERT: C 55 ASP cc_start: 0.8169 (t70) cc_final: 0.7794 (t0) REVERT: C 78 TYR cc_start: 0.8498 (t80) cc_final: 0.8269 (t80) REVERT: C 82 TYR cc_start: 0.8932 (t80) cc_final: 0.8486 (t80) REVERT: D 17 ASN cc_start: 0.8740 (m110) cc_final: 0.8113 (m110) REVERT: D 19 LEU cc_start: 0.9217 (mt) cc_final: 0.8768 (mt) REVERT: D 50 ILE cc_start: 0.9036 (tp) cc_final: 0.8827 (pt) REVERT: D 55 ASP cc_start: 0.8048 (t0) cc_final: 0.6773 (t0) REVERT: D 60 LYS cc_start: 0.8888 (pttt) cc_final: 0.8481 (pttt) REVERT: D 66 LEU cc_start: 0.9589 (mt) cc_final: 0.9172 (mt) REVERT: D 74 GLN cc_start: 0.9057 (mt0) cc_final: 0.8149 (mm-40) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1557 time to fit residues: 44.6495 Evaluate side-chains 176 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.8311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5966 Z= 0.208 Angle : 0.647 8.310 8100 Z= 0.337 Chirality : 0.042 0.193 835 Planarity : 0.004 0.065 1071 Dihedral : 6.024 79.634 784 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.07 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.55 (0.31), residues: 717 helix: 0.97 (0.26), residues: 401 sheet: -0.08 (0.73), residues: 50 loop : -0.33 (0.38), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 156 HIS 0.003 0.001 HIS A 236 PHE 0.016 0.002 PHE D 16 TYR 0.026 0.002 TYR D 9 ARG 0.006 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8151 (m-80) cc_final: 0.7793 (m-80) REVERT: A 77 TRP cc_start: 0.6907 (m-90) cc_final: 0.6551 (m-90) REVERT: A 92 ASP cc_start: 0.6805 (t0) cc_final: 0.6603 (t0) REVERT: A 137 ASN cc_start: 0.7886 (t0) cc_final: 0.6902 (t0) REVERT: A 176 ASN cc_start: 0.9204 (t0) cc_final: 0.8352 (p0) REVERT: A 270 GLU cc_start: 0.7932 (tp30) cc_final: 0.7633 (tp30) REVERT: A 279 ASP cc_start: 0.8411 (p0) cc_final: 0.7888 (p0) REVERT: A 322 LEU cc_start: 0.8536 (tp) cc_final: 0.8212 (tp) REVERT: A 357 LEU cc_start: 0.9264 (tp) cc_final: 0.8794 (tp) REVERT: A 437 ASN cc_start: 0.8570 (p0) cc_final: 0.7653 (p0) REVERT: A 439 ASN cc_start: 0.9361 (t0) cc_final: 0.8307 (t0) REVERT: A 467 MET cc_start: 0.8526 (ttm) cc_final: 0.8201 (ttm) REVERT: B 16 PHE cc_start: 0.8716 (t80) cc_final: 0.8002 (t80) REVERT: B 19 LEU cc_start: 0.8241 (mt) cc_final: 0.7919 (mt) REVERT: B 20 GLN cc_start: 0.7138 (tp-100) cc_final: 0.6207 (tp-100) REVERT: B 89 ILE cc_start: 0.7074 (pt) cc_final: 0.6478 (pt) REVERT: C 13 LEU cc_start: 0.9107 (tp) cc_final: 0.8655 (tp) REVERT: C 16 PHE cc_start: 0.9553 (t80) cc_final: 0.9166 (t80) REVERT: C 24 ASP cc_start: 0.7809 (t0) cc_final: 0.7480 (t0) REVERT: C 41 LEU cc_start: 0.9550 (mt) cc_final: 0.9263 (mt) REVERT: C 82 TYR cc_start: 0.8933 (t80) cc_final: 0.8667 (t80) REVERT: D 15 LEU cc_start: 0.9395 (tp) cc_final: 0.9172 (tp) REVERT: D 17 ASN cc_start: 0.8790 (m110) cc_final: 0.8227 (m110) REVERT: D 19 LEU cc_start: 0.9182 (mt) cc_final: 0.8658 (mt) REVERT: D 55 ASP cc_start: 0.8178 (t0) cc_final: 0.7002 (t0) REVERT: D 60 LYS cc_start: 0.8869 (pttt) cc_final: 0.8333 (pttt) REVERT: D 74 GLN cc_start: 0.9083 (mt0) cc_final: 0.8209 (mm-40) REVERT: D 82 TYR cc_start: 0.8915 (t80) cc_final: 0.8314 (t80) REVERT: D 89 ILE cc_start: 0.9476 (pt) cc_final: 0.9164 (tt) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1526 time to fit residues: 44.5482 Evaluate side-chains 175 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 44 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 ASN D 88 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.8642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5966 Z= 0.179 Angle : 0.667 9.862 8100 Z= 0.346 Chirality : 0.044 0.203 835 Planarity : 0.004 0.042 1071 Dihedral : 6.124 83.136 784 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.93 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.43 (0.31), residues: 717 helix: 0.87 (0.26), residues: 401 sheet: -0.08 (0.73), residues: 52 loop : -0.40 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 156 HIS 0.004 0.001 HIS D 88 PHE 0.017 0.002 PHE D 77 TYR 0.019 0.002 TYR D 9 ARG 0.003 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.8159 (m-80) cc_final: 0.7823 (m-80) REVERT: A 92 ASP cc_start: 0.7083 (t0) cc_final: 0.6520 (t0) REVERT: A 137 ASN cc_start: 0.7894 (t0) cc_final: 0.6989 (t0) REVERT: A 176 ASN cc_start: 0.9214 (t0) cc_final: 0.8311 (p0) REVERT: A 222 GLU cc_start: 0.8799 (tp30) cc_final: 0.8496 (mm-30) REVERT: A 322 LEU cc_start: 0.8580 (tp) cc_final: 0.8202 (tp) REVERT: A 357 LEU cc_start: 0.9314 (tp) cc_final: 0.8879 (tp) REVERT: A 437 ASN cc_start: 0.8567 (p0) cc_final: 0.7530 (p0) REVERT: A 467 MET cc_start: 0.8566 (ttm) cc_final: 0.8155 (ttm) REVERT: B 16 PHE cc_start: 0.8797 (t80) cc_final: 0.8573 (t80) REVERT: B 89 ILE cc_start: 0.7055 (pt) cc_final: 0.6637 (pt) REVERT: C 16 PHE cc_start: 0.9545 (t80) cc_final: 0.9268 (t80) REVERT: C 24 ASP cc_start: 0.8501 (t0) cc_final: 0.7605 (t0) REVERT: C 41 LEU cc_start: 0.9548 (mt) cc_final: 0.9276 (mt) REVERT: C 46 ASN cc_start: 0.7899 (p0) cc_final: 0.7685 (p0) REVERT: C 79 LYS cc_start: 0.8332 (ptpp) cc_final: 0.8042 (pttm) REVERT: C 82 TYR cc_start: 0.8928 (t80) cc_final: 0.8639 (t80) REVERT: D 17 ASN cc_start: 0.8859 (m110) cc_final: 0.8315 (m110) REVERT: D 19 LEU cc_start: 0.9201 (mt) cc_final: 0.8766 (mt) REVERT: D 50 ILE cc_start: 0.9251 (pt) cc_final: 0.8981 (mt) REVERT: D 55 ASP cc_start: 0.7891 (t0) cc_final: 0.6697 (t0) REVERT: D 60 LYS cc_start: 0.8800 (pttt) cc_final: 0.8359 (pttt) REVERT: D 74 GLN cc_start: 0.9102 (mt0) cc_final: 0.8196 (mm110) REVERT: D 82 TYR cc_start: 0.8824 (t80) cc_final: 0.8077 (t80) REVERT: D 89 ILE cc_start: 0.9432 (pt) cc_final: 0.9231 (tt) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.1665 time to fit residues: 45.8196 Evaluate side-chains 171 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.9094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5966 Z= 0.201 Angle : 0.710 10.020 8100 Z= 0.368 Chirality : 0.044 0.199 835 Planarity : 0.004 0.043 1071 Dihedral : 6.186 87.759 784 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.28 % Allowed : 2.93 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.33 (0.31), residues: 717 helix: 0.80 (0.26), residues: 401 sheet: -0.25 (0.70), residues: 52 loop : -0.44 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 156 HIS 0.003 0.001 HIS D 88 PHE 0.019 0.002 PHE D 77 TYR 0.027 0.002 TYR C 26 ARG 0.003 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 TRP cc_start: 0.6851 (m-90) cc_final: 0.6634 (m-90) REVERT: A 92 ASP cc_start: 0.7139 (t0) cc_final: 0.6561 (t0) REVERT: A 137 ASN cc_start: 0.7961 (t0) cc_final: 0.7043 (t0) REVERT: A 176 ASN cc_start: 0.9220 (t0) cc_final: 0.8363 (p0) REVERT: A 222 GLU cc_start: 0.8839 (tp30) cc_final: 0.8555 (mm-30) REVERT: A 270 GLU cc_start: 0.7632 (tp30) cc_final: 0.7332 (tp30) REVERT: A 271 MET cc_start: 0.8230 (mmp) cc_final: 0.7836 (mmm) REVERT: A 279 ASP cc_start: 0.8157 (p0) cc_final: 0.7790 (p0) REVERT: A 322 LEU cc_start: 0.8560 (tp) cc_final: 0.8243 (tp) REVERT: A 357 LEU cc_start: 0.9392 (tp) cc_final: 0.8964 (tp) REVERT: A 437 ASN cc_start: 0.8420 (p0) cc_final: 0.7821 (p0) REVERT: A 454 LEU cc_start: 0.9102 (tp) cc_final: 0.8826 (tp) REVERT: A 467 MET cc_start: 0.8722 (ttm) cc_final: 0.8258 (ttm) REVERT: B 19 LEU cc_start: 0.8248 (mt) cc_final: 0.7884 (mt) REVERT: B 89 ILE cc_start: 0.7325 (pt) cc_final: 0.6844 (pt) REVERT: C 16 PHE cc_start: 0.9510 (t80) cc_final: 0.9246 (t80) REVERT: C 41 LEU cc_start: 0.9580 (mt) cc_final: 0.9342 (mt) REVERT: C 78 TYR cc_start: 0.8544 (t80) cc_final: 0.8217 (t80) REVERT: C 79 LYS cc_start: 0.8334 (ptpp) cc_final: 0.8064 (pttm) REVERT: C 82 TYR cc_start: 0.8923 (t80) cc_final: 0.8667 (t80) REVERT: D 15 LEU cc_start: 0.9372 (tp) cc_final: 0.9155 (tp) REVERT: D 17 ASN cc_start: 0.8838 (m110) cc_final: 0.8260 (m110) REVERT: D 19 LEU cc_start: 0.9165 (mt) cc_final: 0.8703 (mt) REVERT: D 52 PHE cc_start: 0.9293 (t80) cc_final: 0.9089 (t80) REVERT: D 55 ASP cc_start: 0.7874 (t0) cc_final: 0.6736 (t0) REVERT: D 60 LYS cc_start: 0.8884 (pttt) cc_final: 0.8269 (pttt) REVERT: D 74 GLN cc_start: 0.9194 (mt0) cc_final: 0.8291 (mm-40) REVERT: D 78 TYR cc_start: 0.8376 (t80) cc_final: 0.8153 (t80) REVERT: D 82 TYR cc_start: 0.8773 (t80) cc_final: 0.7997 (t80) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.1495 time to fit residues: 41.7915 Evaluate side-chains 167 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 0.3980 chunk 57 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 17 optimal weight: 0.0770 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN D 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.9290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5966 Z= 0.172 Angle : 0.693 9.130 8100 Z= 0.363 Chirality : 0.045 0.206 835 Planarity : 0.004 0.037 1071 Dihedral : 6.007 86.693 784 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.77 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.33 (0.31), residues: 717 helix: 0.77 (0.26), residues: 401 sheet: -0.15 (0.70), residues: 52 loop : -0.41 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 156 HIS 0.001 0.000 HIS B 88 PHE 0.018 0.001 PHE C 90 TYR 0.024 0.002 TYR D 9 ARG 0.003 0.001 ARG A 382 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1434 Ramachandran restraints generated. 717 Oldfield, 0 Emsley, 717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7800 (m-80) cc_final: 0.7599 (m-10) REVERT: A 92 ASP cc_start: 0.7165 (t0) cc_final: 0.6498 (t0) REVERT: A 137 ASN cc_start: 0.7996 (t0) cc_final: 0.6990 (t0) REVERT: A 176 ASN cc_start: 0.9189 (t0) cc_final: 0.8305 (p0) REVERT: A 270 GLU cc_start: 0.7668 (tp30) cc_final: 0.6902 (tp30) REVERT: A 271 MET cc_start: 0.8306 (mmp) cc_final: 0.7716 (mmm) REVERT: A 279 ASP cc_start: 0.8138 (p0) cc_final: 0.7831 (p0) REVERT: A 292 ASP cc_start: 0.7355 (m-30) cc_final: 0.7114 (p0) REVERT: A 322 LEU cc_start: 0.8554 (tp) cc_final: 0.8246 (tp) REVERT: A 357 LEU cc_start: 0.9403 (tp) cc_final: 0.8960 (tp) REVERT: A 437 ASN cc_start: 0.8562 (p0) cc_final: 0.7885 (p0) REVERT: A 440 VAL cc_start: 0.8684 (m) cc_final: 0.7863 (m) REVERT: A 454 LEU cc_start: 0.9022 (tp) cc_final: 0.8763 (tp) REVERT: A 467 MET cc_start: 0.8678 (ttm) cc_final: 0.8300 (ttm) REVERT: B 15 LEU cc_start: 0.8747 (tp) cc_final: 0.8420 (tp) REVERT: B 19 LEU cc_start: 0.8098 (mt) cc_final: 0.7641 (mt) REVERT: B 50 ILE cc_start: 0.9539 (mm) cc_final: 0.9155 (tp) REVERT: B 89 ILE cc_start: 0.7060 (pt) cc_final: 0.6694 (pt) REVERT: C 16 PHE cc_start: 0.9516 (t80) cc_final: 0.9097 (t80) REVERT: C 41 LEU cc_start: 0.9539 (mt) cc_final: 0.9329 (mt) REVERT: C 78 TYR cc_start: 0.8559 (t80) cc_final: 0.8182 (t80) REVERT: C 79 LYS cc_start: 0.8293 (ptpp) cc_final: 0.8025 (pttm) REVERT: D 19 LEU cc_start: 0.9216 (mt) cc_final: 0.8545 (mt) REVERT: D 47 GLU cc_start: 0.9025 (pm20) cc_final: 0.8755 (pm20) REVERT: D 55 ASP cc_start: 0.7869 (t0) cc_final: 0.7278 (t0) REVERT: D 74 GLN cc_start: 0.9099 (mt0) cc_final: 0.8780 (mp10) REVERT: D 78 TYR cc_start: 0.8435 (t80) cc_final: 0.7990 (t80) REVERT: D 82 TYR cc_start: 0.8706 (t80) cc_final: 0.8450 (t80) REVERT: D 90 PHE cc_start: 0.7831 (m-10) cc_final: 0.7414 (m-10) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1615 time to fit residues: 45.8244 Evaluate side-chains 171 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 GLN D 33 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.090424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.071373 restraints weight = 25447.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.073695 restraints weight = 14765.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.075240 restraints weight = 9698.540| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.9555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5966 Z= 0.217 Angle : 0.696 8.588 8100 Z= 0.365 Chirality : 0.045 0.206 835 Planarity : 0.004 0.047 1071 Dihedral : 6.169 88.257 784 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.04 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: 0.08 (0.31), residues: 717 helix: 0.59 (0.26), residues: 408 sheet: -0.15 (0.70), residues: 52 loop : -0.62 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 22 HIS 0.003 0.001 HIS A 363 PHE 0.020 0.002 PHE D 77 TYR 0.030 0.002 TYR C 26 ARG 0.007 0.001 ARG A 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1649.00 seconds wall clock time: 29 minutes 55.31 seconds (1795.31 seconds total)