Starting phenix.real_space_refine on Sun Mar 10 22:05:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/03_2024/8wua_37852.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/03_2024/8wua_37852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/03_2024/8wua_37852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/03_2024/8wua_37852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/03_2024/8wua_37852.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/03_2024/8wua_37852.pdb" } resolution = 3.6 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= 0.003 sd= 0.056 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 38 5.16 5 C 3622 2.51 5 N 888 2.21 5 O 946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 344": "OD1" <-> "OD2" Residue "A PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "A PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 680": "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: 5494 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 675, 5494 Classifications: {'peptide': 675} Link IDs: {'PTRANS': 26, 'TRANS': 648} Chain breaks: 1 Time building chain proxies: 3.23, per 1000 atoms: 0.59 Number of scatterers: 5494 At special positions: 0 Unit cell: (91.1257, 96.6152, 92.2236, 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 38 16.00 O 946 8.00 N 888 7.00 C 3622 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=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 315 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1292 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 2 sheets defined 65.2% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 removed outlier: 4.130A pdb=" N ARG A 18 " --> pdb=" O ALA A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 49 through 75 removed outlier: 3.712A pdb=" N VAL A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 removed outlier: 4.001A 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 158 removed outlier: 3.791A pdb=" N HIS A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 167 removed outlier: 3.822A pdb=" N VAL A 164 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.749A pdb=" N THR A 181 " --> pdb=" O PHE A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 219 removed outlier: 3.793A pdb=" N HIS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 205 " --> pdb=" O VAL A 201 " (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 removed outlier: 4.116A pdb=" N PHE A 307 " --> pdb=" O CYS A 304 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS A 308 " --> pdb=" O GLY A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 308' Processing helix chain 'A' and resid 320 through 341 removed outlier: 3.651A pdb=" N ARG A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 345 removed outlier: 3.753A pdb=" N GLN A 345 " --> pdb=" O VAL A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 342 through 345' Processing helix chain 'A' and resid 357 through 365 Processing helix chain 'A' and resid 415 through 445 removed outlier: 3.915A pdb=" N TRP A 419 " --> pdb=" O GLY A 415 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE A 427 " --> pdb=" O LEU A 423 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N THR A 428 " --> pdb=" O GLY A 424 " (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 515 removed outlier: 4.153A pdb=" N ASN A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLN A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 534 Processing helix chain 'A' and resid 550 through 553 Processing helix chain 'A' and resid 554 through 565 Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 574 through 587 Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.767A pdb=" N LYS A 598 " --> pdb=" O ARG A 594 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 599 " --> pdb=" O ARG A 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 594 through 599' Processing helix chain 'A' and resid 606 through 624 Processing helix chain 'A' and resid 630 through 650 removed outlier: 3.984A pdb=" N PHE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 673 removed outlier: 3.598A pdb=" N ALA A 673 " --> pdb=" O ASN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 690 Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.588A pdb=" N LEU A 698 " --> pdb=" O ALA A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 717 removed outlier: 4.042A pdb=" N PHE A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 262 removed outlier: 3.814A pdb=" N ILE A 232 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A 352 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 396 " --> pdb=" O THR A 233 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 299 301 hydrogen bonds defined for protein. 891 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: 1.47 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1673 1.35 - 1.46: 1428 1.46 - 1.58: 2487 1.58 - 1.70: 2 1.70 - 1.81: 53 Bond restraints: 5643 Sorted by residual: bond pdb=" CB PRO A 439 " pdb=" CG PRO A 439 " ideal model delta sigma weight residual 1.492 1.654 -0.162 5.00e-02 4.00e+02 1.05e+01 bond pdb=" CB PRO A 576 " pdb=" CG PRO A 576 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.88e+00 bond pdb=" N PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 1.473 1.498 -0.025 1.40e-02 5.10e+03 3.15e+00 bond pdb=" N PRO A 439 " pdb=" CA PRO A 439 " ideal model delta sigma weight residual 1.470 1.449 0.021 1.34e-02 5.57e+03 2.55e+00 bond pdb=" CG PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 1.503 1.450 0.053 3.40e-02 8.65e+02 2.46e+00 ... (remaining 5638 not shown) Histogram of bond angle deviations from ideal: 95.86 - 103.48: 67 103.48 - 111.10: 2130 111.10 - 118.72: 2321 118.72 - 126.34: 3045 126.34 - 133.96: 102 Bond angle restraints: 7665 Sorted by residual: angle pdb=" CA PRO A 439 " pdb=" N PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 112.00 95.86 16.14 1.40e+00 5.10e-01 1.33e+02 angle pdb=" CA PRO A 576 " pdb=" N PRO A 576 " pdb=" CD PRO A 576 " ideal model delta sigma weight residual 112.00 101.38 10.62 1.40e+00 5.10e-01 5.75e+01 angle pdb=" N PRO A 439 " pdb=" CD PRO A 439 " pdb=" CG PRO A 439 " ideal model delta sigma weight residual 103.20 95.89 7.31 1.50e+00 4.44e-01 2.38e+01 angle pdb=" CA MET A 327 " pdb=" CB MET A 327 " pdb=" CG MET A 327 " ideal model delta sigma weight residual 114.10 122.70 -8.60 2.00e+00 2.50e-01 1.85e+01 angle pdb=" CA LEU A 471 " pdb=" CB LEU A 471 " pdb=" CG LEU A 471 " ideal model delta sigma weight residual 116.30 130.57 -14.27 3.50e+00 8.16e-02 1.66e+01 ... (remaining 7660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 2943 18.00 - 36.00: 273 36.00 - 54.00: 85 54.00 - 72.00: 5 72.00 - 90.00: 7 Dihedral angle restraints: 3313 sinusoidal: 1321 harmonic: 1992 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 -20.15 -65.85 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS A 32 " pdb=" SG CYS A 32 " pdb=" SG CYS A 546 " pdb=" CB CYS A 546 " ideal model delta sinusoidal sigma weight residual 93.00 36.01 56.99 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CA ASP A 366 " pdb=" C ASP A 366 " pdb=" N PHE A 367 " pdb=" CA PHE A 367 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3310 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 752 0.057 - 0.115: 115 0.115 - 0.172: 5 0.172 - 0.229: 1 0.229 - 0.286: 2 Chirality restraints: 875 Sorted by residual: chirality pdb=" CA PRO A 439 " pdb=" N PRO A 439 " pdb=" C PRO A 439 " pdb=" CB PRO A 439 " both_signs ideal model delta sigma weight residual False 2.72 2.43 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA PRO A 576 " pdb=" N PRO A 576 " pdb=" C PRO A 576 " pdb=" CB PRO A 576 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA MET A 327 " pdb=" N MET A 327 " pdb=" C MET A 327 " pdb=" CB MET A 327 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.42e-01 ... (remaining 872 not shown) Planarity restraints: 941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 438 " -0.084 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO A 439 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 575 " -0.070 5.00e-02 4.00e+02 9.88e-02 1.56e+01 pdb=" N PRO A 576 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 576 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 576 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 529 " -0.017 2.00e-02 2.50e+03 1.94e-02 6.59e+00 pdb=" CG PHE A 529 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 529 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 529 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 529 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 529 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 529 " -0.000 2.00e-02 2.50e+03 ... (remaining 938 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 65 2.66 - 3.22: 5218 3.22 - 3.78: 8354 3.78 - 4.34: 10099 4.34 - 4.90: 16539 Nonbonded interactions: 40275 Sorted by model distance: nonbonded pdb=" O TRP A 531 " pdb=" OG1 THR A 536 " model vdw 2.105 2.440 nonbonded pdb=" O ALA A 694 " pdb=" OG1 THR A 697 " model vdw 2.321 2.440 nonbonded pdb=" NE1 TRP A 418 " pdb=" OE2 GLU A 490 " model vdw 2.378 2.520 nonbonded pdb=" NZ LYS A 371 " pdb=" O VAL A 397 " model vdw 2.381 2.520 nonbonded pdb=" OE1 GLN A 465 " pdb=" ND2 ASN A 558 " model vdw 2.383 2.520 ... (remaining 40270 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: 0.900 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: 3.720 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 18.520 Find NCS groups from input model: 0.150 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5848 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 : 0.004 0.162 5643 Z= 0.208 Angle : 0.750 16.137 7665 Z= 0.376 Chirality : 0.041 0.286 875 Planarity : 0.006 0.114 941 Dihedral : 15.346 89.998 2015 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.49 % Allowed : 23.03 % Favored : 76.48 % 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: 0.31 (0.33), residues: 671 helix: 1.41 (0.27), residues: 399 sheet: 0.65 (1.91), residues: 10 loop : -1.80 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 131 HIS 0.003 0.001 HIS A 648 PHE 0.045 0.001 PHE A 529 TYR 0.014 0.001 TYR A 203 ARG 0.003 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.6903 (mpp) cc_final: 0.6329 (pmm) REVERT: A 413 ILE cc_start: 0.6200 (mt) cc_final: 0.5987 (pt) REVERT: A 513 MET cc_start: 0.8271 (tmm) cc_final: 0.7846 (tmm) outliers start: 3 outliers final: 2 residues processed: 78 average time/residue: 0.1381 time to fit residues: 15.2154 Evaluate side-chains 74 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 0.0470 chunk 34 optimal weight: 0.0010 chunk 27 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 overall best weight: 0.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 5643 Z= 0.146 Angle : 0.568 10.875 7665 Z= 0.266 Chirality : 0.039 0.143 875 Planarity : 0.004 0.044 941 Dihedral : 4.248 46.294 733 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.96 % Allowed : 20.89 % Favored : 76.15 % 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: 0.33 (0.34), residues: 671 helix: 1.46 (0.27), residues: 408 sheet: 0.12 (1.42), residues: 17 loop : -1.99 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 395 HIS 0.003 0.001 HIS A 196 PHE 0.031 0.001 PHE A 529 TYR 0.015 0.001 TYR A 203 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 327 MET cc_start: 0.6745 (mpp) cc_final: 0.6336 (ptp) REVERT: A 349 MET cc_start: 0.4696 (ptt) cc_final: 0.4466 (ptt) REVERT: A 413 ILE cc_start: 0.6415 (OUTLIER) cc_final: 0.6159 (pt) REVERT: A 437 THR cc_start: 0.6393 (m) cc_final: 0.6169 (t) outliers start: 18 outliers final: 11 residues processed: 93 average time/residue: 0.1264 time to fit residues: 16.9271 Evaluate side-chains 92 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 654 TYR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5643 Z= 0.187 Angle : 0.598 11.341 7665 Z= 0.283 Chirality : 0.039 0.141 875 Planarity : 0.004 0.040 941 Dihedral : 3.902 35.630 731 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.93 % Allowed : 21.22 % Favored : 73.85 % 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: 0.43 (0.34), residues: 671 helix: 1.58 (0.27), residues: 402 sheet: 0.08 (1.45), residues: 17 loop : -1.95 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 395 HIS 0.003 0.001 HIS A 196 PHE 0.036 0.001 PHE A 529 TYR 0.012 0.001 TYR A 203 ARG 0.005 0.001 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 96 time to evaluate : 0.668 Fit side-chains REVERT: A 74 ARG cc_start: 0.4566 (ptm160) cc_final: 0.4124 (tpt170) REVERT: A 170 LEU cc_start: 0.7183 (tt) cc_final: 0.6958 (tt) REVERT: A 186 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8802 (tp) REVERT: A 265 ASN cc_start: 0.8685 (t0) cc_final: 0.8484 (t0) REVERT: A 327 MET cc_start: 0.7078 (mpp) cc_final: 0.6767 (ptp) REVERT: A 409 LYS cc_start: 0.7970 (pttt) cc_final: 0.7643 (pttp) REVERT: A 413 ILE cc_start: 0.7102 (OUTLIER) cc_final: 0.6810 (pt) REVERT: A 513 MET cc_start: 0.8189 (tmm) cc_final: 0.7454 (tmm) REVERT: A 683 TYR cc_start: 0.7370 (t80) cc_final: 0.6987 (t80) outliers start: 30 outliers final: 12 residues processed: 115 average time/residue: 0.1307 time to fit residues: 21.1220 Evaluate side-chains 101 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 87 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 508 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 61 optimal weight: 0.0370 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 0.0000 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6365 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5643 Z= 0.137 Angle : 0.594 14.419 7665 Z= 0.274 Chirality : 0.039 0.143 875 Planarity : 0.003 0.034 941 Dihedral : 3.526 17.341 729 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.77 % Allowed : 21.22 % Favored : 74.01 % 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: 0.53 (0.34), residues: 671 helix: 1.68 (0.27), residues: 404 sheet: -0.28 (1.40), residues: 17 loop : -1.93 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 131 HIS 0.002 0.001 HIS A 648 PHE 0.036 0.001 PHE A 529 TYR 0.009 0.001 TYR A 624 ARG 0.005 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 96 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.4637 (ptm160) cc_final: 0.4174 (tpt170) REVERT: A 186 LEU cc_start: 0.9040 (tp) cc_final: 0.8794 (tt) REVERT: A 270 ILE cc_start: 0.7626 (mm) cc_final: 0.7313 (mm) REVERT: A 413 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7147 (pt) REVERT: A 449 PHE cc_start: 0.7873 (m-80) cc_final: 0.5946 (t80) REVERT: A 544 LEU cc_start: 0.8158 (pt) cc_final: 0.7729 (pp) REVERT: A 683 TYR cc_start: 0.7443 (t80) cc_final: 0.6881 (t80) outliers start: 29 outliers final: 18 residues processed: 111 average time/residue: 0.1158 time to fit residues: 18.6885 Evaluate side-chains 110 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 91 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.2980 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 GLN A 643 HIS A 664 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5643 Z= 0.166 Angle : 0.605 10.140 7665 Z= 0.281 Chirality : 0.041 0.238 875 Planarity : 0.003 0.034 941 Dihedral : 3.621 18.337 729 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 5.10 % Allowed : 22.04 % Favored : 72.86 % 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: 0.71 (0.34), residues: 671 helix: 1.87 (0.27), residues: 397 sheet: -0.31 (1.42), residues: 16 loop : -1.83 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.003 0.001 HIS A 213 PHE 0.043 0.001 PHE A 529 TYR 0.012 0.001 TYR A 31 ARG 0.002 0.000 ARG A 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 97 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.7210 (m-80) cc_final: 0.6733 (m-80) REVERT: A 74 ARG cc_start: 0.4604 (ptm160) cc_final: 0.4084 (tpt170) REVERT: A 186 LEU cc_start: 0.9079 (tp) cc_final: 0.8820 (tt) REVERT: A 270 ILE cc_start: 0.8283 (mm) cc_final: 0.7964 (mm) REVERT: A 405 ASP cc_start: 0.7582 (p0) cc_final: 0.7262 (p0) outliers start: 31 outliers final: 23 residues processed: 114 average time/residue: 0.1227 time to fit residues: 20.1287 Evaluate side-chains 116 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 532 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.6008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5643 Z= 0.176 Angle : 0.636 10.678 7665 Z= 0.297 Chirality : 0.042 0.198 875 Planarity : 0.003 0.034 941 Dihedral : 3.772 16.088 729 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 4.93 % Allowed : 22.70 % Favored : 72.37 % 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: 0.63 (0.35), residues: 671 helix: 1.79 (0.27), residues: 397 sheet: -0.28 (1.30), residues: 17 loop : -1.84 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.003 0.001 HIS A 213 PHE 0.042 0.001 PHE A 529 TYR 0.010 0.001 TYR A 203 ARG 0.002 0.000 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 89 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 TYR cc_start: 0.7311 (m-80) cc_final: 0.6871 (m-10) REVERT: A 74 ARG cc_start: 0.4434 (ptm160) cc_final: 0.3952 (tpt170) REVERT: A 162 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8192 (mm) REVERT: A 186 LEU cc_start: 0.9067 (tp) cc_final: 0.8755 (tt) REVERT: A 270 ILE cc_start: 0.8329 (mm) cc_final: 0.8036 (mm) REVERT: A 427 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7003 (t80) REVERT: A 496 SER cc_start: 0.9039 (m) cc_final: 0.8628 (p) REVERT: A 502 MET cc_start: 0.7826 (tpp) cc_final: 0.7585 (tpp) REVERT: A 544 LEU cc_start: 0.8312 (pt) cc_final: 0.7959 (pp) outliers start: 30 outliers final: 22 residues processed: 107 average time/residue: 0.1234 time to fit residues: 18.9193 Evaluate side-chains 106 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.0060 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.6352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5643 Z= 0.156 Angle : 0.621 9.961 7665 Z= 0.286 Chirality : 0.041 0.190 875 Planarity : 0.003 0.035 941 Dihedral : 3.671 17.716 729 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.11 % Allowed : 24.84 % Favored : 71.05 % 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: 0.68 (0.35), residues: 671 helix: 1.79 (0.27), residues: 406 sheet: -0.30 (1.40), residues: 16 loop : -1.87 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.003 0.001 HIS A 196 PHE 0.046 0.001 PHE A 529 TYR 0.019 0.001 TYR A 559 ARG 0.001 0.000 ARG A 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 90 time to evaluate : 0.647 Fit side-chains REVERT: A 31 TYR cc_start: 0.7347 (m-80) cc_final: 0.6918 (m-10) REVERT: A 74 ARG cc_start: 0.4599 (ptm160) cc_final: 0.4132 (tpt170) REVERT: A 186 LEU cc_start: 0.9077 (tp) cc_final: 0.8747 (tt) REVERT: A 270 ILE cc_start: 0.8386 (mm) cc_final: 0.8105 (mm) REVERT: A 349 MET cc_start: 0.7180 (ptm) cc_final: 0.6886 (ptp) REVERT: A 427 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.6991 (t80) REVERT: A 496 SER cc_start: 0.9012 (m) cc_final: 0.8639 (p) REVERT: A 502 MET cc_start: 0.7888 (tpp) cc_final: 0.7647 (tpp) outliers start: 25 outliers final: 21 residues processed: 104 average time/residue: 0.1272 time to fit residues: 18.7616 Evaluate side-chains 104 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 395 TRP Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.0770 chunk 47 optimal weight: 0.0040 overall best weight: 0.3550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.6489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5643 Z= 0.141 Angle : 0.638 9.932 7665 Z= 0.294 Chirality : 0.040 0.206 875 Planarity : 0.003 0.034 941 Dihedral : 3.644 16.302 729 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.95 % Allowed : 25.00 % Favored : 71.05 % 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: 0.66 (0.35), residues: 671 helix: 1.75 (0.27), residues: 406 sheet: -0.30 (1.38), residues: 16 loop : -1.82 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 473 HIS 0.002 0.000 HIS A 196 PHE 0.046 0.001 PHE A 529 TYR 0.014 0.001 TYR A 559 ARG 0.001 0.000 ARG A 296 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 0.668 Fit side-chains revert: symmetry clash REVERT: A 31 TYR cc_start: 0.7223 (m-80) cc_final: 0.6769 (m-10) REVERT: A 74 ARG cc_start: 0.4670 (ptm160) cc_final: 0.4310 (tpt170) REVERT: A 162 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8222 (mm) REVERT: A 186 LEU cc_start: 0.9069 (tp) cc_final: 0.8739 (tt) REVERT: A 270 ILE cc_start: 0.8378 (mm) cc_final: 0.8084 (mm) REVERT: A 349 MET cc_start: 0.6645 (ptm) cc_final: 0.6424 (ptp) REVERT: A 427 PHE cc_start: 0.7906 (OUTLIER) cc_final: 0.7021 (t80) REVERT: A 496 SER cc_start: 0.8921 (m) cc_final: 0.8532 (p) REVERT: A 502 MET cc_start: 0.7886 (tpp) cc_final: 0.7677 (tpp) REVERT: A 670 GLN cc_start: 0.8519 (tp40) cc_final: 0.8222 (tt0) outliers start: 24 outliers final: 18 residues processed: 103 average time/residue: 0.1165 time to fit residues: 17.5055 Evaluate side-chains 104 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 0.0870 chunk 56 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.6943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5643 Z= 0.173 Angle : 0.674 12.459 7665 Z= 0.311 Chirality : 0.042 0.212 875 Planarity : 0.003 0.035 941 Dihedral : 3.737 17.508 729 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.44 % Allowed : 24.67 % Favored : 70.89 % 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: 0.58 (0.35), residues: 671 helix: 1.62 (0.27), residues: 411 sheet: -0.41 (1.34), residues: 17 loop : -1.79 (0.41), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.003 0.001 HIS A 196 PHE 0.044 0.001 PHE A 529 TYR 0.018 0.001 TYR A 559 ARG 0.004 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 91 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 31 TYR cc_start: 0.7342 (m-80) cc_final: 0.6874 (m-10) REVERT: A 74 ARG cc_start: 0.4284 (ptm160) cc_final: 0.4044 (tpt170) REVERT: A 186 LEU cc_start: 0.9055 (tp) cc_final: 0.8635 (tt) REVERT: A 270 ILE cc_start: 0.8426 (mm) cc_final: 0.8132 (mm) REVERT: A 427 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7039 (t80) REVERT: A 496 SER cc_start: 0.8949 (m) cc_final: 0.8555 (p) REVERT: A 502 MET cc_start: 0.7913 (tpp) cc_final: 0.7701 (tpp) outliers start: 27 outliers final: 22 residues processed: 109 average time/residue: 0.1287 time to fit residues: 20.1578 Evaluate side-chains 107 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 0.0570 chunk 14 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5643 Z= 0.149 Angle : 0.690 10.483 7665 Z= 0.315 Chirality : 0.041 0.243 875 Planarity : 0.003 0.036 941 Dihedral : 3.755 16.159 729 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.62 % Allowed : 26.15 % Favored : 70.23 % 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: 0.60 (0.34), residues: 671 helix: 1.68 (0.27), residues: 403 sheet: -0.30 (1.27), residues: 17 loop : -1.77 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 194 HIS 0.002 0.001 HIS A 196 PHE 0.047 0.001 PHE A 529 TYR 0.015 0.001 TYR A 559 ARG 0.002 0.000 ARG A 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 87 time to evaluate : 0.660 Fit side-chains revert: symmetry clash REVERT: A 31 TYR cc_start: 0.7244 (m-80) cc_final: 0.6769 (m-10) REVERT: A 156 LEU cc_start: 0.9262 (tp) cc_final: 0.8967 (pp) REVERT: A 186 LEU cc_start: 0.9038 (tp) cc_final: 0.8627 (tt) REVERT: A 270 ILE cc_start: 0.8425 (mm) cc_final: 0.8126 (mm) REVERT: A 427 PHE cc_start: 0.7904 (OUTLIER) cc_final: 0.7126 (t80) REVERT: A 496 SER cc_start: 0.8923 (m) cc_final: 0.8526 (p) REVERT: A 585 MET cc_start: 0.1869 (tmm) cc_final: 0.0379 (mmm) outliers start: 22 outliers final: 20 residues processed: 101 average time/residue: 0.1268 time to fit residues: 18.2875 Evaluate side-chains 105 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 220 TYR Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 367 PHE Chi-restraints excluded: chain A residue 427 PHE Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 578 LEU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 670 GLN Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 702 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 5.9990 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 42 optimal weight: 0.0070 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 669 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 670 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.138201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.108822 restraints weight = 13961.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.112541 restraints weight = 6852.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.114925 restraints weight = 4346.334| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.7325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5643 Z= 0.165 Angle : 0.666 10.286 7665 Z= 0.309 Chirality : 0.041 0.237 875 Planarity : 0.004 0.035 941 Dihedral : 3.748 17.254 729 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.62 % Allowed : 25.00 % Favored : 71.38 % 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: 0.55 (0.34), residues: 671 helix: 1.68 (0.27), residues: 403 sheet: -0.47 (1.26), residues: 17 loop : -1.87 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.002 0.001 HIS A 196 PHE 0.047 0.001 PHE A 529 TYR 0.017 0.001 TYR A 559 ARG 0.002 0.000 ARG A 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1358.72 seconds wall clock time: 25 minutes 34.58 seconds (1534.58 seconds total)