Starting phenix.real_space_refine on Sun Mar 10 21:13:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehw_28153/03_2024/8ehw_28153.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehw_28153/03_2024/8ehw_28153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehw_28153/03_2024/8ehw_28153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehw_28153/03_2024/8ehw_28153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehw_28153/03_2024/8ehw_28153.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ehw_28153/03_2024/8ehw_28153.pdb" } resolution = 3.8 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= 0.036 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 32 5.16 5 C 3410 2.51 5 N 826 2.21 5 O 882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A TYR 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 319": "OD1" <-> "OD2" Residue "A TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 356": "OE1" <-> "OE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A TYR 485": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 624": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5150 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 630, 5150 Classifications: {'peptide': 630} Link IDs: {'PTRANS': 25, 'TRANS': 604} Chain breaks: 2 Time building chain proxies: 3.28, per 1000 atoms: 0.64 Number of scatterers: 5150 At special positions: 0 Unit cell: (97.35, 107.25, 75.9, 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 32 16.00 O 882 8.00 N 826 7.00 C 3410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 32 " - pdb=" SG CYS A 546 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 315 " distance=2.80 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: 1.91 Conformation dependent library (CDL) restraints added in 908.1 milliseconds 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 70.8% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 45 through 48 removed outlier: 3.722A pdb=" N GLY A 48 " --> pdb=" O VAL A 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 45 through 48' Processing helix chain 'A' and resid 49 through 75 removed outlier: 3.593A pdb=" N VAL A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 3.750A pdb=" N ILE A 120 " --> pdb=" O TRP A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 167 removed outlier: 3.966A pdb=" N HIS A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N CYS A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 177 through 182 Processing helix chain 'A' and resid 191 through 219 removed outlier: 4.165A pdb=" N LEU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 205 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE A 218 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 252 Processing helix chain 'A' and resid 266 through 294 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 320 through 342 removed outlier: 3.546A pdb=" N ARG A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 368 removed outlier: 3.822A pdb=" N ALA A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 391 removed outlier: 3.585A pdb=" N LEU A 390 " --> pdb=" O HIS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 395 Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 415 through 445 removed outlier: 3.522A pdb=" N TRP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR A 428 " --> pdb=" O GLY A 424 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 434 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N THR A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 466 through 491 Proline residue: A 480 - end of helix Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 499 through 515 removed outlier: 3.645A pdb=" N PHE A 509 " --> pdb=" O LYS A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 534 removed outlier: 3.682A pdb=" N SER A 519 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 552 Processing helix chain 'A' and resid 553 through 565 removed outlier: 4.298A pdb=" N VAL A 557 " --> pdb=" O GLY A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 574 through 587 removed outlier: 3.526A pdb=" N MET A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 601 Processing helix chain 'A' and resid 606 through 624 removed outlier: 3.740A pdb=" N TYR A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 650 removed outlier: 4.038A pdb=" N PHE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 672 removed outlier: 4.045A pdb=" N LEU A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 690 removed outlier: 3.743A pdb=" N ILE A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.943A pdb=" N LEU A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 264 removed outlier: 5.626A pdb=" N VAL A 257 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR A 353 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASP A 259 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE A 351 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLN A 261 " --> pdb=" O MET A 349 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N MET A 349 " --> pdb=" O GLN A 261 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 263 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 299 306 hydrogen bonds defined for protein. 873 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: 1.39 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1339 1.34 - 1.46: 1155 1.46 - 1.58: 2751 1.58 - 1.70: 0 1.70 - 1.82: 47 Bond restraints: 5292 Sorted by residual: bond pdb=" N VAL A 451 " pdb=" CA VAL A 451 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N VAL A 342 " pdb=" CA VAL A 342 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.38e+00 bond pdb=" N LYS A 453 " pdb=" CA LYS A 453 " ideal model delta sigma weight residual 1.460 1.481 -0.021 7.10e-03 1.98e+04 8.35e+00 bond pdb=" N CYS A 32 " pdb=" CA CYS A 32 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.25e-02 6.40e+03 7.64e+00 bond pdb=" N VAL A 266 " pdb=" CA VAL A 266 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.08e+00 ... (remaining 5287 not shown) Histogram of bond angle deviations from ideal: 96.14 - 103.80: 66 103.80 - 111.47: 2287 111.47 - 119.14: 1999 119.14 - 126.80: 2758 126.80 - 134.47: 81 Bond angle restraints: 7191 Sorted by residual: angle pdb=" C VAL A 342 " pdb=" CA VAL A 342 " pdb=" CB VAL A 342 " ideal model delta sigma weight residual 111.29 100.02 11.27 1.64e+00 3.72e-01 4.73e+01 angle pdb=" C LEU A 641 " pdb=" CA LEU A 641 " pdb=" CB LEU A 641 " ideal model delta sigma weight residual 110.81 121.73 -10.92 1.60e+00 3.91e-01 4.66e+01 angle pdb=" N VAL A 342 " pdb=" CA VAL A 342 " pdb=" C VAL A 342 " ideal model delta sigma weight residual 109.34 122.94 -13.60 2.08e+00 2.31e-01 4.28e+01 angle pdb=" N LEU A 641 " pdb=" CA LEU A 641 " pdb=" C LEU A 641 " ideal model delta sigma weight residual 111.11 105.62 5.49 1.20e+00 6.94e-01 2.09e+01 angle pdb=" N GLU A 338 " pdb=" CA GLU A 338 " pdb=" C GLU A 338 " ideal model delta sigma weight residual 111.33 116.13 -4.80 1.21e+00 6.83e-01 1.57e+01 ... (remaining 7186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 2651 17.84 - 35.67: 343 35.67 - 53.51: 95 53.51 - 71.34: 9 71.34 - 89.18: 2 Dihedral angle restraints: 3100 sinusoidal: 1236 harmonic: 1864 Sorted by residual: dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 315 " pdb=" CB CYS A 315 " ideal model delta sinusoidal sigma weight residual -86.00 -18.06 -67.94 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" C LEU A 641 " pdb=" N LEU A 641 " pdb=" CA LEU A 641 " pdb=" CB LEU A 641 " ideal model delta harmonic sigma weight residual -122.60 -133.39 10.79 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" CA PRO A 550 " pdb=" C PRO A 550 " pdb=" N ASP A 551 " pdb=" CA ASP A 551 " ideal model delta harmonic sigma weight residual 180.00 -161.67 -18.33 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 660 0.060 - 0.120: 137 0.120 - 0.180: 21 0.180 - 0.240: 5 0.240 - 0.300: 2 Chirality restraints: 825 Sorted by residual: chirality pdb=" CA LEU A 641 " pdb=" N LEU A 641 " pdb=" C LEU A 641 " pdb=" CB LEU A 641 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA TYR A 624 " pdb=" N TYR A 624 " pdb=" C TYR A 624 " pdb=" CB TYR A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE A 270 " pdb=" N ILE A 270 " pdb=" C ILE A 270 " pdb=" CB ILE A 270 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 822 not shown) Planarity restraints: 877 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 338 " -0.020 2.00e-02 2.50e+03 4.08e-02 1.66e+01 pdb=" CD GLU A 338 " 0.070 2.00e-02 2.50e+03 pdb=" OE1 GLU A 338 " -0.025 2.00e-02 2.50e+03 pdb=" OE2 GLU A 338 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 341 " -0.034 2.00e-02 2.50e+03 2.57e-02 9.89e+00 pdb=" CG HIS A 341 " 0.028 2.00e-02 2.50e+03 pdb=" ND1 HIS A 341 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 HIS A 341 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 HIS A 341 " -0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS A 341 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 549 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.16e+00 pdb=" N PRO A 550 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 550 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 550 " 0.042 5.00e-02 4.00e+02 ... (remaining 874 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1295 2.79 - 3.32: 5400 3.32 - 3.84: 8746 3.84 - 4.37: 9798 4.37 - 4.90: 16052 Nonbonded interactions: 41291 Sorted by model distance: nonbonded pdb=" N PHE A 47 " pdb=" O TYR A 176 " model vdw 2.262 2.520 nonbonded pdb=" NZ LYS A 448 " pdb=" OD1 ASP A 551 " model vdw 2.354 2.520 nonbonded pdb=" O ARG A 595 " pdb=" NE2 GLN A 599 " model vdw 2.359 2.520 nonbonded pdb=" NH1 ARG A 530 " pdb=" OD2 ASP A 534 " model vdw 2.387 2.520 nonbonded pdb=" O TRP A 194 " pdb=" OG1 THR A 197 " model vdw 2.412 2.440 ... (remaining 41286 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=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: 1.190 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: 3.990 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.000 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 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 : 0.006 0.043 5292 Z= 0.358 Angle : 0.970 13.601 7191 Z= 0.564 Chirality : 0.053 0.300 825 Planarity : 0.007 0.076 877 Dihedral : 16.572 89.180 1884 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.18 % Allowed : 31.23 % Favored : 68.60 % Cbeta Deviations : 0.17 % 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 (0.34), residues: 624 helix: -0.27 (0.26), residues: 386 sheet: 1.22 (1.35), residues: 16 loop : -1.29 (0.46), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP A 422 HIS 0.010 0.001 HIS A 341 PHE 0.035 0.002 PHE A 307 TYR 0.037 0.003 TYR A 323 ARG 0.006 0.001 ARG A 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 115 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 TYR cc_start: 0.8775 (m-80) cc_final: 0.7875 (m-80) REVERT: A 323 TYR cc_start: 0.8960 (t80) cc_final: 0.8142 (t80) REVERT: A 332 LEU cc_start: 0.9428 (tp) cc_final: 0.9214 (mt) REVERT: A 365 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8732 (mmtt) REVERT: A 502 MET cc_start: 0.7755 (tpt) cc_final: 0.7178 (tpt) outliers start: 1 outliers final: 0 residues processed: 116 average time/residue: 0.1791 time to fit residues: 26.2617 Evaluate side-chains 96 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.0670 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN A 450 ASN ** A 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5292 Z= 0.279 Angle : 0.694 9.717 7191 Z= 0.346 Chirality : 0.044 0.216 825 Planarity : 0.004 0.040 877 Dihedral : 4.577 20.281 681 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.09 % Allowed : 28.25 % Favored : 66.67 % 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: 0.36 (0.35), residues: 624 helix: 0.90 (0.27), residues: 391 sheet: 0.39 (1.12), residues: 22 loop : -0.94 (0.47), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 681 HIS 0.005 0.001 HIS A 341 PHE 0.014 0.001 PHE A 199 TYR 0.021 0.002 TYR A 286 ARG 0.005 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 TYR cc_start: 0.8923 (t80) cc_final: 0.8690 (t80) REVERT: A 324 TYR cc_start: 0.8994 (m-10) cc_final: 0.8582 (m-10) REVERT: A 327 MET cc_start: 0.9209 (mtp) cc_final: 0.8947 (mtm) REVERT: A 333 GLU cc_start: 0.8843 (tt0) cc_final: 0.8157 (tp30) outliers start: 29 outliers final: 11 residues processed: 126 average time/residue: 0.1391 time to fit residues: 23.6380 Evaluate side-chains 103 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.0870 chunk 47 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 51 optimal weight: 30.0000 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5292 Z= 0.177 Angle : 0.670 13.253 7191 Z= 0.320 Chirality : 0.042 0.132 825 Planarity : 0.004 0.036 877 Dihedral : 4.359 18.393 681 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.44 % Allowed : 27.37 % Favored : 67.19 % 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: 0.69 (0.35), residues: 624 helix: 1.12 (0.27), residues: 389 sheet: 0.40 (1.11), residues: 22 loop : -0.67 (0.48), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 681 HIS 0.004 0.001 HIS A 341 PHE 0.020 0.001 PHE A 680 TYR 0.017 0.002 TYR A 286 ARG 0.003 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7279 (t0) cc_final: 0.6422 (t0) REVERT: A 286 TYR cc_start: 0.8997 (m-80) cc_final: 0.8693 (m-10) REVERT: A 327 MET cc_start: 0.9205 (mtp) cc_final: 0.8970 (mtm) REVERT: A 333 GLU cc_start: 0.8939 (tt0) cc_final: 0.8129 (tp30) REVERT: A 606 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7573 (pm20) outliers start: 31 outliers final: 14 residues processed: 127 average time/residue: 0.1313 time to fit residues: 22.8107 Evaluate side-chains 112 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 97 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 653 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 30 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5292 Z= 0.301 Angle : 0.721 13.732 7191 Z= 0.344 Chirality : 0.043 0.154 825 Planarity : 0.004 0.034 877 Dihedral : 4.362 18.639 681 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 5.79 % Allowed : 27.37 % Favored : 66.84 % 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: 0.54 (0.35), residues: 624 helix: 0.85 (0.26), residues: 394 sheet: 0.61 (1.07), residues: 22 loop : -0.45 (0.49), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 681 HIS 0.003 0.001 HIS A 341 PHE 0.020 0.001 PHE A 556 TYR 0.025 0.002 TYR A 624 ARG 0.003 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 98 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7471 (t0) cc_final: 0.6555 (t0) REVERT: A 323 TYR cc_start: 0.8936 (t80) cc_final: 0.8649 (t80) REVERT: A 324 TYR cc_start: 0.8209 (m-10) cc_final: 0.7899 (m-10) REVERT: A 327 MET cc_start: 0.9258 (mtp) cc_final: 0.8938 (mtp) REVERT: A 333 GLU cc_start: 0.8997 (tt0) cc_final: 0.8140 (tp30) REVERT: A 435 PHE cc_start: 0.7968 (m-10) cc_final: 0.7712 (m-10) REVERT: A 443 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7530 (mp) REVERT: A 502 MET cc_start: 0.7840 (tpt) cc_final: 0.7373 (tpt) REVERT: A 570 MET cc_start: 0.8670 (tpt) cc_final: 0.8231 (tpt) REVERT: A 606 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7819 (pm20) outliers start: 33 outliers final: 21 residues processed: 120 average time/residue: 0.1381 time to fit residues: 22.5958 Evaluate side-chains 121 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 50 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 0.0000 chunk 20 optimal weight: 5.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5292 Z= 0.180 Angle : 0.670 13.593 7191 Z= 0.316 Chirality : 0.041 0.140 825 Planarity : 0.004 0.035 877 Dihedral : 4.302 18.306 681 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.44 % Allowed : 27.89 % Favored : 66.67 % 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: 0.80 (0.35), residues: 624 helix: 1.04 (0.27), residues: 389 sheet: 0.56 (1.05), residues: 22 loop : -0.29 (0.48), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 681 HIS 0.003 0.001 HIS A 341 PHE 0.022 0.001 PHE A 63 TYR 0.021 0.002 TYR A 286 ARG 0.002 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 102 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7452 (t0) cc_final: 0.6366 (t0) REVERT: A 323 TYR cc_start: 0.8938 (t80) cc_final: 0.8601 (t80) REVERT: A 324 TYR cc_start: 0.8319 (m-10) cc_final: 0.8037 (m-10) REVERT: A 327 MET cc_start: 0.9251 (mtp) cc_final: 0.8856 (mtp) REVERT: A 333 GLU cc_start: 0.8993 (tt0) cc_final: 0.8133 (tp30) REVERT: A 422 TRP cc_start: 0.8129 (OUTLIER) cc_final: 0.7240 (t60) REVERT: A 502 MET cc_start: 0.7850 (tpt) cc_final: 0.7501 (tpt) REVERT: A 606 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7720 (pm20) outliers start: 31 outliers final: 19 residues processed: 127 average time/residue: 0.1320 time to fit residues: 22.8860 Evaluate side-chains 117 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 422 TRP Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 15 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5292 Z= 0.231 Angle : 0.711 13.106 7191 Z= 0.335 Chirality : 0.043 0.162 825 Planarity : 0.003 0.035 877 Dihedral : 4.274 18.392 681 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 5.09 % Allowed : 29.65 % Favored : 65.26 % 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: 0.67 (0.35), residues: 624 helix: 0.99 (0.27), residues: 394 sheet: 0.40 (0.99), residues: 22 loop : -0.45 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 681 HIS 0.003 0.001 HIS A 214 PHE 0.018 0.001 PHE A 63 TYR 0.018 0.002 TYR A 624 ARG 0.003 0.000 ARG A 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7502 (t0) cc_final: 0.6510 (t0) REVERT: A 323 TYR cc_start: 0.8940 (t80) cc_final: 0.8685 (t80) REVERT: A 324 TYR cc_start: 0.8407 (m-10) cc_final: 0.8132 (m-10) REVERT: A 327 MET cc_start: 0.9263 (mtp) cc_final: 0.8858 (mtm) REVERT: A 333 GLU cc_start: 0.8990 (tt0) cc_final: 0.8062 (tp30) REVERT: A 443 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7433 (mp) REVERT: A 502 MET cc_start: 0.7885 (tpt) cc_final: 0.7417 (tpt) REVERT: A 570 MET cc_start: 0.8634 (tpt) cc_final: 0.8331 (tpt) REVERT: A 606 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7706 (pm20) outliers start: 29 outliers final: 19 residues processed: 118 average time/residue: 0.1284 time to fit residues: 20.9805 Evaluate side-chains 116 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 0.0170 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.0070 chunk 37 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5292 Z= 0.179 Angle : 0.691 14.021 7191 Z= 0.325 Chirality : 0.042 0.151 825 Planarity : 0.003 0.036 877 Dihedral : 4.255 18.142 681 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.09 % Allowed : 29.65 % Favored : 65.26 % 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 (0.35), residues: 624 helix: 0.86 (0.26), residues: 406 sheet: 0.32 (1.01), residues: 22 loop : -0.30 (0.50), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 681 HIS 0.002 0.000 HIS A 341 PHE 0.018 0.001 PHE A 556 TYR 0.014 0.001 TYR A 624 ARG 0.002 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 101 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7510 (t0) cc_final: 0.6544 (t0) REVERT: A 327 MET cc_start: 0.9269 (mtp) cc_final: 0.8959 (ptm) REVERT: A 333 GLU cc_start: 0.8979 (tt0) cc_final: 0.8078 (tp30) REVERT: A 443 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7405 (mp) REVERT: A 460 ASN cc_start: 0.7748 (t0) cc_final: 0.7414 (t0) REVERT: A 502 MET cc_start: 0.7835 (tpt) cc_final: 0.7547 (tpt) REVERT: A 606 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7619 (pm20) outliers start: 29 outliers final: 20 residues processed: 122 average time/residue: 0.1219 time to fit residues: 20.8235 Evaluate side-chains 119 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 30.0000 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.0070 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5292 Z= 0.179 Angle : 0.701 14.832 7191 Z= 0.328 Chirality : 0.042 0.155 825 Planarity : 0.003 0.034 877 Dihedral : 4.210 17.862 681 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.74 % Allowed : 30.88 % Favored : 64.39 % 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: 0.82 (0.35), residues: 624 helix: 0.98 (0.26), residues: 400 sheet: 0.21 (0.99), residues: 22 loop : -0.11 (0.51), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 681 HIS 0.003 0.000 HIS A 341 PHE 0.026 0.001 PHE A 680 TYR 0.028 0.002 TYR A 624 ARG 0.002 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7532 (t0) cc_final: 0.6537 (t0) REVERT: A 331 LEU cc_start: 0.9399 (mt) cc_final: 0.9199 (pp) REVERT: A 333 GLU cc_start: 0.8997 (tt0) cc_final: 0.8098 (tp30) REVERT: A 460 ASN cc_start: 0.7751 (t0) cc_final: 0.7377 (t0) REVERT: A 502 MET cc_start: 0.7820 (tpt) cc_final: 0.7440 (tpt) REVERT: A 570 MET cc_start: 0.8620 (tpt) cc_final: 0.8378 (tpt) REVERT: A 571 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8150 (tm-30) REVERT: A 606 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7578 (pm20) outliers start: 27 outliers final: 23 residues processed: 119 average time/residue: 0.1218 time to fit residues: 20.2723 Evaluate side-chains 119 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 353 THR Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 51 optimal weight: 0.0040 chunk 53 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5292 Z= 0.186 Angle : 0.707 15.022 7191 Z= 0.329 Chirality : 0.042 0.154 825 Planarity : 0.003 0.032 877 Dihedral : 4.199 17.755 681 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 4.04 % Allowed : 31.05 % Favored : 64.91 % 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: 0.98 (0.35), residues: 624 helix: 1.18 (0.27), residues: 390 sheet: 0.24 (1.01), residues: 22 loop : -0.15 (0.49), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 681 HIS 0.002 0.000 HIS A 341 PHE 0.020 0.001 PHE A 556 TYR 0.036 0.002 TYR A 324 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7571 (t0) cc_final: 0.6434 (t0) REVERT: A 333 GLU cc_start: 0.9015 (tt0) cc_final: 0.8148 (tp30) REVERT: A 460 ASN cc_start: 0.7762 (t0) cc_final: 0.7388 (t0) REVERT: A 502 MET cc_start: 0.7887 (tpt) cc_final: 0.7442 (tpt) REVERT: A 570 MET cc_start: 0.8613 (tpt) cc_final: 0.8384 (tpt) REVERT: A 606 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7553 (pm20) outliers start: 23 outliers final: 22 residues processed: 110 average time/residue: 0.1217 time to fit residues: 18.7895 Evaluate side-chains 113 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 90 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5292 Z= 0.191 Angle : 0.772 16.920 7191 Z= 0.356 Chirality : 0.043 0.171 825 Planarity : 0.003 0.031 877 Dihedral : 4.216 17.852 681 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.86 % Allowed : 31.93 % Favored : 64.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.35), residues: 624 helix: 1.10 (0.27), residues: 390 sheet: 0.24 (1.02), residues: 22 loop : -0.16 (0.49), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 681 HIS 0.002 0.000 HIS A 341 PHE 0.019 0.001 PHE A 556 TYR 0.025 0.002 TYR A 624 ARG 0.002 0.000 ARG A 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1248 Ramachandran restraints generated. 624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 96 time to evaluate : 0.563 Fit side-chains revert: symmetry clash REVERT: A 185 ASN cc_start: 0.7571 (t0) cc_final: 0.6438 (t0) REVERT: A 327 MET cc_start: 0.9270 (mtm) cc_final: 0.8838 (pmm) REVERT: A 333 GLU cc_start: 0.9013 (tt0) cc_final: 0.8170 (tp30) REVERT: A 349 MET cc_start: 0.6996 (mmp) cc_final: 0.6696 (mmp) REVERT: A 460 ASN cc_start: 0.7738 (t0) cc_final: 0.7389 (t0) REVERT: A 502 MET cc_start: 0.7886 (tpt) cc_final: 0.7444 (tpt) REVERT: A 606 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7892 (mt-10) outliers start: 22 outliers final: 20 residues processed: 113 average time/residue: 0.1293 time to fit residues: 20.2301 Evaluate side-chains 112 residues out of total 570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain A residue 131 TRP Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 199 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 511 ILE Chi-restraints excluded: chain A residue 516 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 606 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 690 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 0.0060 chunk 20 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.169546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121787 restraints weight = 8810.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.121886 restraints weight = 5811.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.122472 restraints weight = 4352.668| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5292 Z= 0.193 Angle : 0.770 16.605 7191 Z= 0.360 Chirality : 0.044 0.230 825 Planarity : 0.003 0.030 877 Dihedral : 4.184 17.773 681 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.04 % Allowed : 31.40 % Favored : 64.56 % 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: 0.76 (0.35), residues: 624 helix: 0.95 (0.26), residues: 397 sheet: 0.63 (1.19), residues: 17 loop : -0.19 (0.50), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 681 HIS 0.002 0.000 HIS A 341 PHE 0.018 0.001 PHE A 63 TYR 0.024 0.002 TYR A 624 ARG 0.002 0.000 ARG A 249 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1346.34 seconds wall clock time: 25 minutes 14.30 seconds (1514.30 seconds total)