Starting phenix.real_space_refine on Fri Aug 2 21:56:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/08_2024/8wua_37852.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/08_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_37852/08_2024/8wua_37852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/08_2024/8wua_37852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/08_2024/8wua_37852.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wua_37852/08_2024/8wua_37852.cif" } 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-5409/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: 4.36, per 1000 atoms: 0.79 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: 2.11 Conformation dependent library (CDL) restraints added in 1.1 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: 0.58 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: 1.41 Time building geometry restraints manager: 2.31 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 3.040 nonbonded pdb=" O ALA A 694 " pdb=" OG1 THR A 697 " model vdw 2.321 3.040 nonbonded pdb=" NE1 TRP A 418 " pdb=" OE2 GLU A 490 " model vdw 2.378 3.120 nonbonded pdb=" NZ LYS A 371 " pdb=" O VAL A 397 " model vdw 2.381 3.120 nonbonded pdb=" OE1 GLN A 465 " pdb=" ND2 ASN A 558 " model vdw 2.383 3.120 ... (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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.070 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.990 ------------------------------------------------------------------------------- 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 : 0.598 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: 0.1393 time to fit residues: 15.5209 Evaluate side-chains 74 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.588 ------------------------------------------------------------------------------- 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: 7.9990 chunk 17 optimal weight: 0.7980 chunk 34 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.6147 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5643 Z= 0.173 Angle : 0.600 10.934 7665 Z= 0.287 Chirality : 0.040 0.140 875 Planarity : 0.004 0.048 941 Dihedral : 4.366 46.647 733 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.45 % Allowed : 20.07 % 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: 0.23 (0.34), residues: 671 helix: 1.36 (0.27), residues: 407 sheet: 0.24 (1.43), residues: 17 loop : -2.00 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 395 HIS 0.006 0.001 HIS A 213 PHE 0.033 0.001 PHE A 529 TYR 0.015 0.001 TYR A 323 ARG 0.004 0.000 ARG A 74 *********************** 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 106 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 85 time to evaluate : 0.633 Fit side-chains REVERT: A 74 ARG cc_start: 0.4751 (ptm160) cc_final: 0.4108 (tpt170) REVERT: A 327 MET cc_start: 0.6932 (mpp) cc_final: 0.6560 (ptp) REVERT: A 413 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6476 (pt) REVERT: A 437 THR cc_start: 0.6319 (m) cc_final: 0.6083 (t) REVERT: A 627 THR cc_start: 0.7849 (m) cc_final: 0.7235 (p) outliers start: 21 outliers final: 11 residues processed: 97 average time/residue: 0.1220 time to fit residues: 17.0415 Evaluate side-chains 93 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE 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 489 LEU Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 578 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 8.9990 chunk 18 optimal weight: 0.9990 chunk 50 optimal weight: 0.0770 chunk 41 optimal weight: 0.0000 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5643 Z= 0.137 Angle : 0.574 11.388 7665 Z= 0.269 Chirality : 0.039 0.131 875 Planarity : 0.003 0.035 941 Dihedral : 3.730 35.148 731 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.29 % Allowed : 21.05 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.34), residues: 671 helix: 1.49 (0.27), residues: 407 sheet: -0.09 (1.38), residues: 17 loop : -1.97 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 131 HIS 0.004 0.001 HIS A 213 PHE 0.036 0.001 PHE A 529 TYR 0.012 0.001 TYR A 362 ARG 0.001 0.000 ARG A 296 *********************** 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 106 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 86 time to evaluate : 0.630 Fit side-chains REVERT: A 74 ARG cc_start: 0.4536 (ptm160) cc_final: 0.4111 (tpt170) REVERT: A 265 ASN cc_start: 0.8477 (t0) cc_final: 0.8227 (t0) REVERT: A 327 MET cc_start: 0.7002 (mpp) cc_final: 0.6724 (ptp) REVERT: A 413 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6684 (pt) REVERT: A 437 THR cc_start: 0.6503 (m) cc_final: 0.6280 (t) REVERT: A 513 MET cc_start: 0.8182 (tmm) cc_final: 0.7556 (tmm) REVERT: A 627 THR cc_start: 0.7510 (m) cc_final: 0.6955 (p) REVERT: A 683 TYR cc_start: 0.7240 (t80) cc_final: 0.6875 (t80) outliers start: 20 outliers final: 12 residues processed: 99 average time/residue: 0.1180 time to fit residues: 17.0684 Evaluate side-chains 95 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 82 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 162 LEU 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 413 ILE Chi-restraints excluded: chain A residue 435 PHE 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 682 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: 0.5980 chunk 6 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 604 GLN A 664 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5643 Z= 0.187 Angle : 0.601 11.151 7665 Z= 0.294 Chirality : 0.041 0.132 875 Planarity : 0.003 0.034 941 Dihedral : 3.720 17.706 729 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.93 % Allowed : 19.57 % Favored : 75.49 % 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: 1.56 (0.27), residues: 408 sheet: -0.26 (1.36), residues: 17 loop : -1.96 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 395 HIS 0.006 0.001 HIS A 213 PHE 0.037 0.001 PHE A 529 TYR 0.009 0.001 TYR A 624 ARG 0.002 0.000 ARG A 530 *********************** 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 127 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 97 time to evaluate : 0.616 Fit side-chains REVERT: A 74 ARG cc_start: 0.4497 (ptm160) cc_final: 0.3916 (tpt170) REVERT: A 260 VAL cc_start: 0.8998 (t) cc_final: 0.8784 (t) REVERT: A 265 ASN cc_start: 0.8860 (t0) cc_final: 0.8510 (t0) REVERT: A 270 ILE cc_start: 0.8016 (mm) cc_final: 0.7708 (mm) REVERT: A 413 ILE cc_start: 0.7512 (OUTLIER) cc_final: 0.7249 (pt) REVERT: A 449 PHE cc_start: 0.8057 (m-80) cc_final: 0.7560 (m-80) REVERT: A 544 LEU cc_start: 0.8356 (pt) cc_final: 0.7874 (pp) REVERT: A 545 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8148 (tm-30) outliers start: 30 outliers final: 14 residues processed: 115 average time/residue: 0.1211 time to fit residues: 19.8625 Evaluate side-chains 99 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 ILE 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 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 413 ILE Chi-restraints excluded: chain A residue 435 PHE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 611 TYR Chi-restraints excluded: chain A residue 615 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: 0.1980 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 33 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 21 optimal weight: 0.0170 chunk 12 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 overall best weight: 0.3256 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5643 Z= 0.138 Angle : 0.581 10.710 7665 Z= 0.275 Chirality : 0.040 0.260 875 Planarity : 0.003 0.035 941 Dihedral : 3.528 18.005 729 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.12 % Allowed : 24.01 % 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: 0.50 (0.34), residues: 671 helix: 1.61 (0.27), residues: 408 sheet: -0.10 (1.34), residues: 17 loop : -1.92 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 131 HIS 0.004 0.001 HIS A 213 PHE 0.044 0.001 PHE A 529 TYR 0.009 0.001 TYR A 31 ARG 0.003 0.000 ARG A 326 *********************** 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 106 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.4651 (ptm160) cc_final: 0.4197 (tpt170) REVERT: A 270 ILE cc_start: 0.8221 (mm) cc_final: 0.7923 (mm) REVERT: A 413 ILE cc_start: 0.7468 (OUTLIER) cc_final: 0.7192 (pt) REVERT: A 449 PHE cc_start: 0.8098 (m-80) cc_final: 0.7560 (m-80) REVERT: A 502 MET cc_start: 0.7357 (tpp) cc_final: 0.7049 (tpp) REVERT: A 544 LEU cc_start: 0.8095 (pt) cc_final: 0.7658 (pp) REVERT: A 627 THR cc_start: 0.7662 (m) cc_final: 0.7100 (p) REVERT: A 683 TYR cc_start: 0.7728 (t80) cc_final: 0.7109 (t80) outliers start: 19 outliers final: 16 residues processed: 97 average time/residue: 0.1236 time to fit residues: 17.2378 Evaluate side-chains 102 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 85 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP 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 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 413 ILE 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 702 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 7 optimal weight: 0.0370 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.5533 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= 0.170 Angle : 0.606 10.471 7665 Z= 0.291 Chirality : 0.041 0.208 875 Planarity : 0.003 0.035 941 Dihedral : 3.561 17.665 729 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 4.61 % Allowed : 23.52 % Favored : 71.88 % 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: 0.61 (0.34), residues: 671 helix: 1.70 (0.27), residues: 411 sheet: -0.13 (1.32), residues: 17 loop : -1.93 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 395 HIS 0.005 0.001 HIS A 213 PHE 0.041 0.001 PHE A 529 TYR 0.009 0.001 TYR A 624 ARG 0.002 0.000 ARG A 74 *********************** 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 118 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 74 ARG cc_start: 0.4650 (ptm160) cc_final: 0.4042 (tpt170) REVERT: A 270 ILE cc_start: 0.8379 (mm) cc_final: 0.8086 (mm) REVERT: A 427 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7019 (t80) REVERT: A 502 MET cc_start: 0.7570 (tpp) cc_final: 0.7264 (tpp) REVERT: A 683 TYR cc_start: 0.7979 (t80) cc_final: 0.7726 (t80) outliers start: 28 outliers final: 19 residues processed: 105 average time/residue: 0.1318 time to fit residues: 19.7350 Evaluate side-chains 102 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 82 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 TRP 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 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 427 PHE Chi-restraints excluded: chain A residue 435 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 500 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.7258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5643 Z= 0.234 Angle : 0.670 9.795 7665 Z= 0.324 Chirality : 0.043 0.197 875 Planarity : 0.004 0.035 941 Dihedral : 4.068 17.782 729 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.61 % Allowed : 23.85 % Favored : 71.55 % 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: 0.40 (0.34), residues: 671 helix: 1.53 (0.27), residues: 410 sheet: -1.10 (1.43), residues: 12 loop : -1.90 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 473 HIS 0.006 0.001 HIS A 213 PHE 0.044 0.002 PHE A 529 TYR 0.015 0.002 TYR A 559 ARG 0.003 0.001 ARG A 72 *********************** 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 125 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 0.770 Fit side-chains REVERT: A 232 ILE cc_start: 0.7981 (mt) cc_final: 0.7699 (tt) REVERT: A 427 PHE cc_start: 0.7909 (OUTLIER) cc_final: 0.6966 (t80) REVERT: A 496 SER cc_start: 0.9127 (m) cc_final: 0.8717 (p) REVERT: A 668 VAL cc_start: 0.8249 (t) cc_final: 0.7909 (p) outliers start: 28 outliers final: 22 residues processed: 118 average time/residue: 0.1234 time to fit residues: 20.7104 Evaluate side-chains 107 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain A residue 137 ILE 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 230 LEU 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 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 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: 0.6980 chunk 31 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 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 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.7593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5643 Z= 0.186 Angle : 0.692 11.059 7665 Z= 0.327 Chirality : 0.042 0.202 875 Planarity : 0.003 0.034 941 Dihedral : 3.898 17.524 729 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.95 % Allowed : 27.30 % Favored : 68.75 % 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: 0.40 (0.34), residues: 671 helix: 1.45 (0.27), residues: 413 sheet: -0.94 (1.40), residues: 12 loop : -1.81 (0.40), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.004 0.001 HIS A 196 PHE 0.048 0.001 PHE A 529 TYR 0.023 0.001 TYR A 683 ARG 0.001 0.000 ARG A 74 *********************** 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 109 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.642 Fit side-chains REVERT: A 232 ILE cc_start: 0.8019 (mt) cc_final: 0.7741 (tt) REVERT: A 380 GLU cc_start: 0.8453 (pm20) cc_final: 0.7987 (mp0) REVERT: A 427 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6991 (t80) REVERT: A 496 SER cc_start: 0.9177 (m) cc_final: 0.8770 (p) REVERT: A 585 MET cc_start: 0.2007 (tmm) cc_final: 0.0390 (mmt) REVERT: A 668 VAL cc_start: 0.8022 (t) cc_final: 0.7710 (p) outliers start: 24 outliers final: 21 residues processed: 101 average time/residue: 0.1150 time to fit residues: 17.1929 Evaluate side-chains 105 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 83 time to evaluate : 0.632 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 LEU 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 451 VAL 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 702 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.0980 chunk 63 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 343 GLN A 670 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.7956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5643 Z= 0.195 Angle : 0.706 14.013 7665 Z= 0.334 Chirality : 0.043 0.222 875 Planarity : 0.003 0.034 941 Dihedral : 3.892 17.499 729 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.28 % Allowed : 26.48 % Favored : 69.24 % 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: 0.47 (0.34), residues: 671 helix: 1.55 (0.27), residues: 404 sheet: -0.88 (1.40), residues: 12 loop : -1.73 (0.40), residues: 255 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 0.044 0.001 PHE A 529 TYR 0.020 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 109 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ILE cc_start: 0.8106 (mt) cc_final: 0.7872 (tt) REVERT: A 380 GLU cc_start: 0.8410 (pm20) cc_final: 0.7873 (mp0) REVERT: A 427 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7111 (t80) REVERT: A 496 SER cc_start: 0.9074 (m) cc_final: 0.8671 (p) REVERT: A 585 MET cc_start: 0.1787 (tmm) cc_final: 0.0259 (mmt) outliers start: 26 outliers final: 21 residues processed: 101 average time/residue: 0.1159 time to fit residues: 17.2961 Evaluate side-chains 100 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 78 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 152 VAL 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 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 435 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 702 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 49 optimal weight: 0.2980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.8072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5643 Z= 0.173 Angle : 0.720 17.022 7665 Z= 0.333 Chirality : 0.043 0.227 875 Planarity : 0.003 0.034 941 Dihedral : 3.880 16.780 729 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.12 % Allowed : 27.30 % Favored : 69.57 % 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: 0.47 (0.34), residues: 671 helix: 1.58 (0.27), residues: 404 sheet: -0.93 (1.36), residues: 12 loop : -1.77 (0.40), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.002 0.001 HIS A 648 PHE 0.047 0.001 PHE A 529 TYR 0.019 0.001 TYR A 559 ARG 0.001 0.000 ARG A 530 ********************** 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 102 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 83 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 ILE cc_start: 0.8114 (mt) cc_final: 0.7861 (tt) REVERT: A 436 LEU cc_start: 0.6847 (tt) cc_final: 0.6590 (tt) REVERT: A 496 SER cc_start: 0.9050 (m) cc_final: 0.8648 (p) REVERT: A 585 MET cc_start: 0.1604 (tmm) cc_final: 0.0144 (mmt) outliers start: 19 outliers final: 18 residues processed: 97 average time/residue: 0.1195 time to fit residues: 16.8289 Evaluate side-chains 97 residues out of total 608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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 50 ILE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 162 LEU 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 246 SER Chi-restraints excluded: chain A residue 367 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 0.0070 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.136104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.106267 restraints weight = 13881.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.109949 restraints weight = 6948.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.112386 restraints weight = 4426.301| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.8245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5643 Z= 0.164 Angle : 0.694 16.142 7665 Z= 0.322 Chirality : 0.042 0.224 875 Planarity : 0.003 0.033 941 Dihedral : 3.815 17.993 729 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.96 % Allowed : 26.97 % Favored : 70.07 % 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: 0.48 (0.34), residues: 671 helix: 1.55 (0.27), residues: 406 sheet: -1.02 (1.33), residues: 12 loop : -1.73 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 473 HIS 0.002 0.001 HIS A 456 PHE 0.048 0.001 PHE A 529 TYR 0.018 0.001 TYR A 559 ARG 0.002 0.000 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.23 seconds wall clock time: 25 minutes 18.40 seconds (1518.40 seconds total)