Starting phenix.real_space_refine on Thu Jan 18 03:04:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c3y_16415/01_2024/8c3y_16415.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c3y_16415/01_2024/8c3y_16415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c3y_16415/01_2024/8c3y_16415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c3y_16415/01_2024/8c3y_16415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c3y_16415/01_2024/8c3y_16415.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c3y_16415/01_2024/8c3y_16415.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.051 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 43 5.16 5 C 4777 2.51 5 N 1319 2.21 5 O 1441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 515": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7580 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 929, 7580 Classifications: {'peptide': 929} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 903} Chain breaks: 12 Time building chain proxies: 4.46, per 1000 atoms: 0.59 Number of scatterers: 7580 At special positions: 0 Unit cell: (74.88, 117.312, 107.328, 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 43 16.00 O 1441 8.00 N 1319 7.00 C 4777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 127 " distance=2.03 Simple disulfide: pdb=" SG CYS A 182 " - pdb=" SG CYS A 281 " distance=2.02 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 435 " distance=2.02 Simple disulfide: pdb=" SG CYS A 324 " - pdb=" SG CYS A 359 " distance=2.04 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 356 " distance=2.04 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 467 " distance=2.03 Simple disulfide: pdb=" SG CYS A 363 " - pdb=" SG CYS A 464 " distance=2.05 Simple disulfide: pdb=" SG CYS A 526 " - pdb=" SG CYS A 614 " distance=2.02 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 553 " distance=2.09 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 608 " distance=2.04 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS A 719 " distance=2.04 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 710 " distance=2.03 Simple disulfide: pdb=" SG CYS A 908 " - pdb=" SG CYS A1000 " 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: 3.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1756 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 3 sheets defined 61.7% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 20 through 42 removed outlier: 3.853A pdb=" N LYS A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.966A pdb=" N ARG A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 150 through 172 Processing helix chain 'A' and resid 179 through 197 Processing helix chain 'A' and resid 212 through 227 Processing helix chain 'A' and resid 227 through 232 removed outlier: 4.131A pdb=" N LEU A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 256 removed outlier: 5.536A pdb=" N GLU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 324 Processing helix chain 'A' and resid 327 through 330 Processing helix chain 'A' and resid 356 through 393 Proline residue: A 365 - end of helix Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 421 through 431 removed outlier: 4.190A pdb=" N GLU A 431 " --> pdb=" O LYS A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 523 Processing helix chain 'A' and resid 523 through 528 Processing helix chain 'A' and resid 571 through 593 Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 604 through 631 removed outlier: 4.150A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 644 Processing helix chain 'A' and resid 648 through 654 removed outlier: 3.570A pdb=" N ASP A 652 " --> pdb=" O ASP A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 666 through 686 Processing helix chain 'A' and resid 690 through 713 removed outlier: 3.932A pdb=" N ALA A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 719 removed outlier: 6.422A pdb=" N GLU A 717 " --> pdb=" O ASN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 763 Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 844 through 848 Processing helix chain 'A' and resid 869 through 892 Processing helix chain 'A' and resid 904 through 924 Processing helix chain 'A' and resid 931 through 952 Processing helix chain 'A' and resid 954 through 962 removed outlier: 3.882A pdb=" N ASN A 958 " --> pdb=" O ILE A 955 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N GLN A 959 " --> pdb=" O LYS A 956 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LYS A 960 " --> pdb=" O ASP A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 967 Processing helix chain 'A' and resid 971 through 994 removed outlier: 5.401A pdb=" N ASP A 984 " --> pdb=" O GLU A 980 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N GLN A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1040 Processing helix chain 'A' and resid 1058 through 1097 Processing helix chain 'A' and resid 1113 through 1126 Processing sheet with id=AA1, first strand: chain 'A' and resid 266 through 267 Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA3, first strand: chain 'A' and resid 503 through 509 removed outlier: 7.006A pdb=" N GLN A 539 " --> pdb=" O GLU A 556 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS A 552 " --> pdb=" O TYR A 543 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1218 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: 2.23 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1475 1.32 - 1.46: 2542 1.46 - 1.59: 3650 1.59 - 1.73: 17 1.73 - 1.87: 50 Bond restraints: 7734 Sorted by residual: bond pdb=" CB TYR A 644 " pdb=" CG TYR A 644 " ideal model delta sigma weight residual 1.512 1.427 0.085 2.20e-02 2.07e+03 1.50e+01 bond pdb=" NE ARG A 215 " pdb=" CZ ARG A 215 " ideal model delta sigma weight residual 1.326 1.368 -0.042 1.10e-02 8.26e+03 1.44e+01 bond pdb=" NE1 TRP A 589 " pdb=" CE2 TRP A 589 " ideal model delta sigma weight residual 1.370 1.329 0.041 1.10e-02 8.26e+03 1.42e+01 bond pdb=" CA TYR A 543 " pdb=" C TYR A 543 " ideal model delta sigma weight residual 1.530 1.488 0.041 1.11e-02 8.12e+03 1.37e+01 bond pdb=" CG ASP A 964 " pdb=" OD2 ASP A 964 " ideal model delta sigma weight residual 1.249 1.179 0.070 1.90e-02 2.77e+03 1.36e+01 ... (remaining 7729 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.70: 130 105.70 - 112.87: 3749 112.87 - 120.03: 3367 120.03 - 127.20: 3059 127.20 - 134.37: 90 Bond angle restraints: 10395 Sorted by residual: angle pdb=" C LEU A 841 " pdb=" N PRO A 842 " pdb=" CA PRO A 842 " ideal model delta sigma weight residual 119.66 125.64 -5.98 7.30e-01 1.88e+00 6.72e+01 angle pdb=" N ILE A1166 " pdb=" CA ILE A1166 " pdb=" C ILE A1166 " ideal model delta sigma weight residual 111.58 120.18 -8.60 1.06e+00 8.90e-01 6.58e+01 angle pdb=" C PRO A 842 " pdb=" N PRO A 843 " pdb=" CA PRO A 843 " ideal model delta sigma weight residual 119.56 127.30 -7.74 1.02e+00 9.61e-01 5.75e+01 angle pdb=" N ILE A 559 " pdb=" CA ILE A 559 " pdb=" C ILE A 559 " ideal model delta sigma weight residual 113.47 106.20 7.27 1.01e+00 9.80e-01 5.18e+01 angle pdb=" C MET A 952 " pdb=" N PRO A 953 " pdb=" CA PRO A 953 " ideal model delta sigma weight residual 120.03 127.09 -7.06 9.90e-01 1.02e+00 5.08e+01 ... (remaining 10390 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 4510 17.87 - 35.74: 156 35.74 - 53.61: 32 53.61 - 71.48: 12 71.48 - 89.35: 8 Dihedral angle restraints: 4718 sinusoidal: 2000 harmonic: 2718 Sorted by residual: dihedral pdb=" SG CYS A 605 " pdb=" CB CYS A 719 " pdb=" SG CYS A 719 " pdb=" CA CYS A 719 " ideal model delta sinusoidal sigma weight residual 79.00 3.44 75.56 1 2.00e+01 2.50e-03 1.80e+01 dihedral pdb=" CB CYS A 340 " pdb=" SG CYS A 340 " pdb=" SG CYS A 467 " pdb=" CB CYS A 467 " ideal model delta sinusoidal sigma weight residual -86.00 -55.46 -30.54 1 1.00e+01 1.00e-02 1.33e+01 dihedral pdb=" CB GLU A 515 " pdb=" CG GLU A 515 " pdb=" CD GLU A 515 " pdb=" OE1 GLU A 515 " ideal model delta sinusoidal sigma weight residual 0.00 -87.18 87.18 1 3.00e+01 1.11e-03 1.01e+01 ... (remaining 4715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 756 0.096 - 0.191: 262 0.191 - 0.287: 51 0.287 - 0.383: 4 0.383 - 0.479: 2 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CB VAL A 839 " pdb=" CA VAL A 839 " pdb=" CG1 VAL A 839 " pdb=" CG2 VAL A 839 " both_signs ideal model delta sigma weight residual False -2.63 -3.11 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB VAL A 472 " pdb=" CA VAL A 472 " pdb=" CG1 VAL A 472 " pdb=" CG2 VAL A 472 " both_signs ideal model delta sigma weight residual False -2.63 -3.06 0.43 2.00e-01 2.50e+01 4.63e+00 chirality pdb=" CA ILE A 647 " pdb=" N ILE A 647 " pdb=" C ILE A 647 " pdb=" CB ILE A 647 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 1072 not shown) Planarity restraints: 1344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 544 " 0.081 2.00e-02 2.50e+03 4.43e-02 3.92e+01 pdb=" CG TYR A 544 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 544 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 544 " -0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR A 544 " -0.023 2.00e-02 2.50e+03 pdb=" CE2 TYR A 544 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR A 544 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 544 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 669 " 0.058 2.00e-02 2.50e+03 2.90e-02 2.11e+01 pdb=" CG TRP A 669 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP A 669 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP A 669 " -0.035 2.00e-02 2.50e+03 pdb=" NE1 TRP A 669 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 669 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 669 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 669 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 669 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 669 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1017 " 0.371 9.50e-02 1.11e+02 1.66e-01 1.69e+01 pdb=" NE ARG A1017 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG A1017 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A1017 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A1017 " 0.012 2.00e-02 2.50e+03 ... (remaining 1341 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1479 2.76 - 3.30: 7897 3.30 - 3.83: 12979 3.83 - 4.37: 15979 4.37 - 4.90: 24659 Nonbonded interactions: 62993 Sorted by model distance: nonbonded pdb=" OD1 ASN A 686 " pdb=" OG1 THR A 689 " model vdw 2.226 2.440 nonbonded pdb=" OG SER A 20 " pdb=" ND2 ASN A 23 " model vdw 2.356 2.520 nonbonded pdb=" O LEU A 645 " pdb=" ND2 ASN A 646 " model vdw 2.362 2.520 nonbonded pdb=" NZ LYS A 745 " pdb=" OD1 ASP A1009 " model vdw 2.372 2.520 nonbonded pdb=" O PHE A 651 " pdb=" O PHE A 654 " model vdw 2.384 3.040 ... (remaining 62988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.900 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.170 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.018 0.100 7734 Z= 1.150 Angle : 1.562 8.860 10395 Z= 1.101 Chirality : 0.097 0.479 1075 Planarity : 0.010 0.166 1344 Dihedral : 10.954 89.353 2920 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.65 % Favored : 96.02 % Rotamer: Outliers : 0.48 % Allowed : 1.45 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.34 (0.25), residues: 904 helix: 0.93 (0.20), residues: 524 sheet: 0.59 (1.04), residues: 23 loop : -0.78 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.008 TRP A 669 HIS 0.007 0.002 HIS A 756 PHE 0.034 0.006 PHE A 615 TYR 0.081 0.008 TYR A 544 ARG 0.007 0.001 ARG A 983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 294 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.5720 (mttt) cc_final: 0.5253 (tttm) REVERT: A 170 VAL cc_start: 0.7961 (m) cc_final: 0.7739 (m) REVERT: A 256 THR cc_start: 0.8987 (p) cc_final: 0.8710 (t) REVERT: A 291 ASN cc_start: 0.8715 (m-40) cc_final: 0.8486 (m-40) REVERT: A 514 LYS cc_start: 0.8747 (tttt) cc_final: 0.8189 (tptm) REVERT: A 647 ILE cc_start: 0.8356 (mt) cc_final: 0.8134 (mt) REVERT: A 883 GLU cc_start: 0.8457 (tt0) cc_final: 0.8059 (pp20) REVERT: A 912 ARG cc_start: 0.8786 (mtt180) cc_final: 0.8578 (ttm110) REVERT: A 991 LYS cc_start: 0.8769 (ptmt) cc_final: 0.8450 (ttmt) REVERT: A 1067 TYR cc_start: 0.9453 (t80) cc_final: 0.9000 (t80) REVERT: A 1084 LYS cc_start: 0.9275 (mttt) cc_final: 0.9064 (mmtt) outliers start: 4 outliers final: 0 residues processed: 298 average time/residue: 0.2594 time to fit residues: 96.3708 Evaluate side-chains 169 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN A 380 GLN A 621 GLN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 648 ASN A 679 GLN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 HIS A 958 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7734 Z= 0.246 Angle : 0.726 9.720 10395 Z= 0.401 Chirality : 0.045 0.185 1075 Planarity : 0.005 0.074 1344 Dihedral : 4.986 19.607 995 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.43 % Favored : 96.46 % Rotamer: Outliers : 3.14 % Allowed : 10.40 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: 0.91 (0.27), residues: 904 helix: 1.50 (0.21), residues: 519 sheet: 0.24 (0.94), residues: 23 loop : -0.67 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 244 HIS 0.005 0.001 HIS A 152 PHE 0.023 0.002 PHE A 458 TYR 0.025 0.002 TYR A1085 ARG 0.009 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.5941 (mttt) cc_final: 0.5543 (tttt) REVERT: A 165 GLU cc_start: 0.8723 (tp30) cc_final: 0.8450 (tp30) REVERT: A 194 ASP cc_start: 0.8457 (m-30) cc_final: 0.7999 (m-30) REVERT: A 243 TRP cc_start: 0.9018 (t60) cc_final: 0.8806 (t60) REVERT: A 256 THR cc_start: 0.8872 (p) cc_final: 0.8607 (t) REVERT: A 307 ASP cc_start: 0.8312 (m-30) cc_final: 0.8092 (m-30) REVERT: A 469 ASP cc_start: 0.8631 (m-30) cc_final: 0.8356 (t0) REVERT: A 514 LYS cc_start: 0.9093 (tttt) cc_final: 0.8736 (tptm) REVERT: A 629 ILE cc_start: 0.8701 (mt) cc_final: 0.8348 (mm) REVERT: A 883 GLU cc_start: 0.8298 (tt0) cc_final: 0.7952 (pp20) REVERT: A 912 ARG cc_start: 0.8763 (mtt180) cc_final: 0.8442 (ttm110) REVERT: A 915 TYR cc_start: 0.8881 (t80) cc_final: 0.8674 (t80) REVERT: A 1008 LEU cc_start: 0.8936 (mt) cc_final: 0.8729 (mt) REVERT: A 1010 ASP cc_start: 0.8419 (p0) cc_final: 0.8197 (p0) outliers start: 26 outliers final: 17 residues processed: 207 average time/residue: 0.2287 time to fit residues: 61.0954 Evaluate side-chains 178 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 161 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 619 VAL Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1098 ASN Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 0.0470 chunk 25 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 56 optimal weight: 0.0570 chunk 23 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 HIS ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7734 Z= 0.205 Angle : 0.660 9.061 10395 Z= 0.357 Chirality : 0.042 0.147 1075 Planarity : 0.005 0.091 1344 Dihedral : 4.885 37.019 995 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.09 % Favored : 95.69 % Rotamer: Outliers : 3.63 % Allowed : 13.18 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.86 (0.27), residues: 904 helix: 1.52 (0.21), residues: 511 sheet: 0.06 (0.99), residues: 21 loop : -0.72 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 244 HIS 0.004 0.001 HIS A 173 PHE 0.034 0.002 PHE A1118 TYR 0.027 0.002 TYR A1067 ARG 0.008 0.001 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.9170 (mmmt) cc_final: 0.8669 (mmmt) REVERT: A 163 LYS cc_start: 0.5410 (mttt) cc_final: 0.5177 (tttt) REVERT: A 180 GLU cc_start: 0.8314 (tt0) cc_final: 0.8045 (mt-10) REVERT: A 256 THR cc_start: 0.8826 (p) cc_final: 0.8533 (t) REVERT: A 301 TRP cc_start: 0.9155 (m-10) cc_final: 0.8937 (m-10) REVERT: A 469 ASP cc_start: 0.8580 (m-30) cc_final: 0.8327 (t0) REVERT: A 883 GLU cc_start: 0.8237 (tt0) cc_final: 0.7847 (pp20) REVERT: A 912 ARG cc_start: 0.8726 (mtt180) cc_final: 0.8482 (ttm110) REVERT: A 913 TYR cc_start: 0.8660 (m-80) cc_final: 0.8390 (m-10) REVERT: A 963 ASP cc_start: 0.8587 (m-30) cc_final: 0.7574 (t0) REVERT: A 1010 ASP cc_start: 0.8450 (p0) cc_final: 0.8168 (p0) REVERT: A 1018 TRP cc_start: 0.9054 (m-10) cc_final: 0.8835 (m-10) REVERT: A 1072 LYS cc_start: 0.9511 (pttm) cc_final: 0.9250 (pttm) outliers start: 30 outliers final: 21 residues processed: 185 average time/residue: 0.2132 time to fit residues: 51.9193 Evaluate side-chains 168 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 HIS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 4.9990 chunk 62 optimal weight: 0.0060 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 88 optimal weight: 9.9990 chunk 79 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 74 optimal weight: 5.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 ASN A 222 ASN ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 393 HIS A 507 ASN A 621 GLN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 714 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7734 Z= 0.199 Angle : 0.625 8.664 10395 Z= 0.342 Chirality : 0.042 0.158 1075 Planarity : 0.004 0.057 1344 Dihedral : 4.748 38.741 995 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.54 % Favored : 95.24 % Rotamer: Outliers : 3.99 % Allowed : 15.48 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.78 (0.27), residues: 904 helix: 1.53 (0.22), residues: 506 sheet: -0.30 (1.06), residues: 22 loop : -0.83 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 244 HIS 0.003 0.001 HIS A 18 PHE 0.020 0.001 PHE A1118 TYR 0.030 0.002 TYR A1067 ARG 0.004 0.001 ARG A 975 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8655 (pp20) cc_final: 0.8264 (pp20) REVERT: A 194 ASP cc_start: 0.8713 (m-30) cc_final: 0.8485 (m-30) REVERT: A 234 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8156 (mt) REVERT: A 256 THR cc_start: 0.8772 (p) cc_final: 0.8495 (t) REVERT: A 469 ASP cc_start: 0.8590 (m-30) cc_final: 0.8305 (t0) REVERT: A 625 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.5863 (mp0) REVERT: A 638 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.7746 (p0) REVERT: A 883 GLU cc_start: 0.8239 (tt0) cc_final: 0.7814 (pp20) REVERT: A 912 ARG cc_start: 0.8702 (mtt180) cc_final: 0.8421 (ttm110) REVERT: A 963 ASP cc_start: 0.8619 (m-30) cc_final: 0.7591 (t0) REVERT: A 1072 LYS cc_start: 0.9505 (pttm) cc_final: 0.9238 (pttm) REVERT: A 1126 ASN cc_start: 0.8061 (OUTLIER) cc_final: 0.7532 (t0) outliers start: 33 outliers final: 22 residues processed: 183 average time/residue: 0.2096 time to fit residues: 50.6193 Evaluate side-chains 175 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 149 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 0.0270 chunk 36 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.0270 chunk 29 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7734 Z= 0.183 Angle : 0.617 9.047 10395 Z= 0.332 Chirality : 0.042 0.161 1075 Planarity : 0.004 0.043 1344 Dihedral : 4.666 38.991 995 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.98 % Favored : 94.80 % Rotamer: Outliers : 3.99 % Allowed : 16.81 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.27), residues: 904 helix: 1.53 (0.22), residues: 515 sheet: -0.02 (1.08), residues: 22 loop : -0.85 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP A 244 HIS 0.002 0.000 HIS A 393 PHE 0.030 0.002 PHE A 633 TYR 0.024 0.002 TYR A1067 ARG 0.003 0.000 ARG A 975 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8669 (p0) cc_final: 0.8167 (p0) REVERT: A 180 GLU cc_start: 0.8352 (tt0) cc_final: 0.8078 (mt-10) REVERT: A 256 THR cc_start: 0.8749 (p) cc_final: 0.8453 (t) REVERT: A 469 ASP cc_start: 0.8607 (m-30) cc_final: 0.8307 (t0) REVERT: A 625 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5602 (mp0) REVERT: A 638 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7764 (p0) REVERT: A 883 GLU cc_start: 0.8179 (tt0) cc_final: 0.7775 (pp20) REVERT: A 912 ARG cc_start: 0.8720 (mtt180) cc_final: 0.8491 (ttm110) REVERT: A 963 ASP cc_start: 0.8667 (m-30) cc_final: 0.7626 (t0) REVERT: A 975 ARG cc_start: 0.8397 (mtm180) cc_final: 0.8154 (mtm-85) REVERT: A 1067 TYR cc_start: 0.9477 (t80) cc_final: 0.9254 (t80) REVERT: A 1069 LYS cc_start: 0.9839 (mttt) cc_final: 0.9631 (mttm) REVERT: A 1072 LYS cc_start: 0.9484 (pttm) cc_final: 0.9247 (pttm) REVERT: A 1126 ASN cc_start: 0.8043 (OUTLIER) cc_final: 0.7589 (t0) outliers start: 33 outliers final: 21 residues processed: 188 average time/residue: 0.2159 time to fit residues: 53.3727 Evaluate side-chains 164 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1117 ASP Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 0.0270 chunk 17 optimal weight: 0.0770 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 46 optimal weight: 0.0770 chunk 85 optimal weight: 2.9990 overall best weight: 0.8358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 ASN A 417 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 HIS A 936 ASN A 967 ASN ** A 982 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7734 Z= 0.194 Angle : 0.630 9.429 10395 Z= 0.343 Chirality : 0.042 0.165 1075 Planarity : 0.004 0.038 1344 Dihedral : 4.618 37.633 995 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.98 % Favored : 94.80 % Rotamer: Outliers : 4.35 % Allowed : 18.62 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.79 (0.28), residues: 904 helix: 1.49 (0.22), residues: 521 sheet: -0.16 (1.01), residues: 22 loop : -0.86 (0.33), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP A 244 HIS 0.002 0.001 HIS A 702 PHE 0.021 0.002 PHE A 220 TYR 0.021 0.001 TYR A1067 ARG 0.008 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 155 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8669 (p0) cc_final: 0.8197 (p0) REVERT: A 180 GLU cc_start: 0.8387 (tt0) cc_final: 0.8125 (mt-10) REVERT: A 256 THR cc_start: 0.8728 (p) cc_final: 0.8428 (t) REVERT: A 370 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8727 (tp) REVERT: A 469 ASP cc_start: 0.8599 (m-30) cc_final: 0.8283 (t0) REVERT: A 625 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5531 (mp0) REVERT: A 638 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.7791 (p0) REVERT: A 883 GLU cc_start: 0.8163 (tt0) cc_final: 0.7742 (pp20) REVERT: A 963 ASP cc_start: 0.8699 (m-30) cc_final: 0.7641 (t0) REVERT: A 1072 LYS cc_start: 0.9458 (pttm) cc_final: 0.9199 (pttm) REVERT: A 1126 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7710 (t0) REVERT: A 1130 LYS cc_start: 0.8978 (mttt) cc_final: 0.8684 (tmtt) outliers start: 36 outliers final: 28 residues processed: 179 average time/residue: 0.2034 time to fit residues: 48.0668 Evaluate side-chains 168 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 136 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 506 ILE Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 656 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 HIS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1009 ASP Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1064 CYS Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 65 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7734 Z= 0.186 Angle : 0.635 11.655 10395 Z= 0.341 Chirality : 0.042 0.251 1075 Planarity : 0.004 0.038 1344 Dihedral : 4.599 36.964 995 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.31 % Favored : 94.47 % Rotamer: Outliers : 3.99 % Allowed : 19.23 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.72 (0.28), residues: 904 helix: 1.44 (0.22), residues: 521 sheet: -0.34 (1.00), residues: 22 loop : -0.88 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP A 244 HIS 0.002 0.001 HIS A 43 PHE 0.014 0.001 PHE A 220 TYR 0.023 0.001 TYR A 643 ARG 0.007 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASN cc_start: 0.8658 (p0) cc_final: 0.8185 (p0) REVERT: A 256 THR cc_start: 0.8692 (p) cc_final: 0.8397 (t) REVERT: A 469 ASP cc_start: 0.8602 (m-30) cc_final: 0.8261 (t0) REVERT: A 625 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5540 (mp0) REVERT: A 630 MET cc_start: 0.8843 (mmm) cc_final: 0.8494 (mmm) REVERT: A 883 GLU cc_start: 0.8132 (tt0) cc_final: 0.7782 (tp30) REVERT: A 963 ASP cc_start: 0.8689 (m-30) cc_final: 0.7642 (t0) REVERT: A 1126 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7745 (t0) REVERT: A 1130 LYS cc_start: 0.8915 (mttt) cc_final: 0.8689 (tmtt) outliers start: 33 outliers final: 25 residues processed: 173 average time/residue: 0.1564 time to fit residues: 36.2724 Evaluate side-chains 167 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 651 PHE Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 HIS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1016 LEU Chi-restraints excluded: chain A residue 1040 LYS Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1126 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 HIS ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.6594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7734 Z= 0.290 Angle : 0.675 11.173 10395 Z= 0.369 Chirality : 0.044 0.202 1075 Planarity : 0.005 0.040 1344 Dihedral : 4.680 35.042 995 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.42 % Favored : 93.36 % Rotamer: Outliers : 3.87 % Allowed : 19.71 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.65 (0.27), residues: 904 helix: 1.44 (0.21), residues: 522 sheet: -0.60 (0.98), residues: 24 loop : -1.01 (0.34), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP A 244 HIS 0.004 0.001 HIS A 702 PHE 0.028 0.002 PHE A 220 TYR 0.027 0.002 TYR A 643 ARG 0.007 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 THR cc_start: 0.8737 (p) cc_final: 0.8418 (t) REVERT: A 469 ASP cc_start: 0.8674 (m-30) cc_final: 0.8160 (t0) REVERT: A 514 LYS cc_start: 0.9192 (tptm) cc_final: 0.8762 (tptm) REVERT: A 625 GLU cc_start: 0.6539 (OUTLIER) cc_final: 0.5629 (mp0) REVERT: A 883 GLU cc_start: 0.8204 (tt0) cc_final: 0.7820 (tp30) REVERT: A 1130 LYS cc_start: 0.8980 (mttt) cc_final: 0.8687 (tmtt) outliers start: 32 outliers final: 25 residues processed: 173 average time/residue: 0.2030 time to fit residues: 46.9840 Evaluate side-chains 164 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 HIS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1095 TYR Chi-restraints excluded: chain A residue 1115 VAL Chi-restraints excluded: chain A residue 1117 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 5.9990 chunk 49 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 HIS ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 ASN ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.6766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7734 Z= 0.198 Angle : 0.676 12.174 10395 Z= 0.359 Chirality : 0.043 0.206 1075 Planarity : 0.004 0.037 1344 Dihedral : 4.645 34.953 995 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.42 % Favored : 94.36 % Rotamer: Outliers : 3.51 % Allowed : 21.04 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.75 (0.28), residues: 904 helix: 1.49 (0.21), residues: 514 sheet: -0.27 (0.99), residues: 24 loop : -0.88 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A 244 HIS 0.002 0.001 HIS A 18 PHE 0.024 0.002 PHE A 220 TYR 0.025 0.002 TYR A 643 ARG 0.006 0.001 ARG A 300 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LYS cc_start: 0.5639 (tttt) cc_final: 0.5430 (tttt) REVERT: A 256 THR cc_start: 0.8656 (p) cc_final: 0.8379 (t) REVERT: A 514 LYS cc_start: 0.9139 (tptm) cc_final: 0.8706 (tptm) REVERT: A 515 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7381 (mm-30) REVERT: A 625 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5494 (mp0) REVERT: A 693 GLU cc_start: 0.8025 (pm20) cc_final: 0.7786 (pm20) REVERT: A 883 GLU cc_start: 0.8085 (tt0) cc_final: 0.7730 (tp30) REVERT: A 963 ASP cc_start: 0.8630 (m-30) cc_final: 0.7530 (t0) REVERT: A 1069 LYS cc_start: 0.9816 (mttt) cc_final: 0.9590 (mttm) REVERT: A 1072 LYS cc_start: 0.9520 (pptt) cc_final: 0.9217 (pttm) REVERT: A 1130 LYS cc_start: 0.8939 (mttt) cc_final: 0.8657 (tmtt) outliers start: 29 outliers final: 22 residues processed: 172 average time/residue: 0.1958 time to fit residues: 45.5141 Evaluate side-chains 168 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 227 ASN Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 HIS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 984 ASP Chi-restraints excluded: chain A residue 1064 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9980 chunk 60 optimal weight: 0.3980 chunk 91 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 8.9990 chunk 22 optimal weight: 0.2980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7734 Z= 0.188 Angle : 0.702 12.150 10395 Z= 0.367 Chirality : 0.045 0.333 1075 Planarity : 0.004 0.041 1344 Dihedral : 4.650 34.572 995 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.53 % Favored : 94.25 % Rotamer: Outliers : 2.54 % Allowed : 22.13 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.78 (0.28), residues: 904 helix: 1.50 (0.22), residues: 514 sheet: -0.28 (1.01), residues: 24 loop : -0.84 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP A 244 HIS 0.002 0.000 HIS A 18 PHE 0.031 0.002 PHE A 656 TYR 0.036 0.002 TYR A1067 ARG 0.006 0.001 ARG A 300 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1808 Ramachandran restraints generated. 904 Oldfield, 0 Emsley, 904 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 149 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 ASN cc_start: 0.8346 (t0) cc_final: 0.7854 (p0) REVERT: A 256 THR cc_start: 0.8640 (p) cc_final: 0.8383 (t) REVERT: A 514 LYS cc_start: 0.9116 (tptm) cc_final: 0.8629 (tptm) REVERT: A 515 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 625 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5638 (mp0) REVERT: A 883 GLU cc_start: 0.8050 (tt0) cc_final: 0.7692 (tp30) REVERT: A 963 ASP cc_start: 0.8600 (m-30) cc_final: 0.7524 (t0) REVERT: A 1069 LYS cc_start: 0.9812 (mttt) cc_final: 0.9584 (mttm) REVERT: A 1072 LYS cc_start: 0.9505 (pptt) cc_final: 0.9198 (pttm) REVERT: A 1130 LYS cc_start: 0.8930 (mttt) cc_final: 0.8645 (tmtt) outliers start: 21 outliers final: 19 residues processed: 161 average time/residue: 0.2096 time to fit residues: 45.1819 Evaluate side-chains 160 residues out of total 827 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain A residue 220 PHE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 576 ASP Chi-restraints excluded: chain A residue 625 GLU Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 655 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 754 ILE Chi-restraints excluded: chain A residue 756 HIS Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 984 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 75 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 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 = 0.3868 r_free = 0.3868 target = 0.106780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082296 restraints weight = 21144.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.085755 restraints weight = 11670.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088074 restraints weight = 7985.455| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.7049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7734 Z= 0.195 Angle : 0.702 12.044 10395 Z= 0.369 Chirality : 0.044 0.325 1075 Planarity : 0.004 0.040 1344 Dihedral : 4.560 34.285 995 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.53 % Favored : 94.25 % Rotamer: Outliers : 2.78 % Allowed : 22.61 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 0.86 (0.28), residues: 904 helix: 1.55 (0.22), residues: 513 sheet: -0.28 (1.03), residues: 24 loop : -0.77 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.003 TRP A 244 HIS 0.002 0.001 HIS A 173 PHE 0.026 0.002 PHE A 525 TYR 0.022 0.002 TYR A 643 ARG 0.006 0.001 ARG A 300 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.01 seconds wall clock time: 46 minutes 21.39 seconds (2781.39 seconds total)