Starting phenix.real_space_refine on Mon Mar 11 03:58:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/03_2024/8iwr_35777_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/03_2024/8iwr_35777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/03_2024/8iwr_35777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/03_2024/8iwr_35777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/03_2024/8iwr_35777_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/03_2024/8iwr_35777_trim_updated.pdb" } resolution = 3.52 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= 0.019 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: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 P 3 5.49 5 Mg 1 5.21 5 S 52 5.16 5 C 4371 2.51 5 N 1149 2.21 5 O 1294 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 427": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6871 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 6838 Classifications: {'peptide': 893} Link IDs: {'PTRANS': 35, 'TRANS': 857} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 1, ' MG': 1, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.26, per 1000 atoms: 0.62 Number of scatterers: 6871 At special positions: 0 Unit cell: (115.08, 100.8, 107.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 1 19.99 S 52 16.00 P 3 15.00 Mg 1 11.99 O 1294 8.00 N 1149 7.00 C 4371 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 3.08 Conformation dependent library (CDL) restraints added in 1.3 seconds 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 11 sheets defined 48.0% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 31 through 38 Processing helix chain 'A' and resid 48 through 58 Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 82 through 96 Processing helix chain 'A' and resid 101 through 130 Processing helix chain 'A' and resid 152 through 154 No H-bonds generated for 'chain 'A' and resid 152 through 154' Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 257 through 286 Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 310 through 328 removed outlier: 3.749A pdb=" N LYS A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 341 removed outlier: 4.170A pdb=" N GLU A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 411 Processing helix chain 'A' and resid 425 through 437 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 504 through 518 removed outlier: 4.221A pdb=" N VAL A 509 " --> pdb=" O GLN A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 562 removed outlier: 4.021A pdb=" N SER A 562 " --> pdb=" O THR A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 596 through 601 Processing helix chain 'A' and resid 605 through 613 removed outlier: 4.218A pdb=" N GLN A 609 " --> pdb=" O GLN A 605 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE A 610 " --> pdb=" O GLN A 606 " (cutoff:3.500A) Proline residue: A 612 - end of helix Processing helix chain 'A' and resid 622 through 635 Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 667 through 672 Processing helix chain 'A' and resid 684 through 722 Processing helix chain 'A' and resid 732 through 741 Processing helix chain 'A' and resid 744 through 750 Processing helix chain 'A' and resid 773 through 797 Processing helix chain 'A' and resid 805 through 824 Processing helix chain 'A' and resid 842 through 859 Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 875 through 908 removed outlier: 3.662A pdb=" N SER A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL A 888 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N CYS A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 138 through 143 removed outlier: 3.747A pdb=" N THR A 150 " --> pdb=" O CYS A 139 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 160 through 163 removed outlier: 3.572A pdb=" N GLU A 177 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 346 through 348 Processing sheet with id= D, first strand: chain 'A' and resid 374 through 376 removed outlier: 3.886A pdb=" N GLU A 385 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 360 through 367 removed outlier: 3.579A pdb=" N THR A 361 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY A 543 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE A 365 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU A 541 " --> pdb=" O ILE A 365 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N THR A 367 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N LEU A 539 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU A 527 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A 476 " --> pdb=" O CYS A 465 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N CYS A 465 " --> pdb=" O ILE A 476 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 462 " --> pdb=" O TYR A 452 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA A 450 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N VAL A 466 " --> pdb=" O ARG A 448 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ARG A 448 " --> pdb=" O VAL A 466 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 492 through 494 Processing sheet with id= G, first strand: chain 'A' and resid 522 through 524 Processing sheet with id= H, first strand: chain 'A' and resid 659 through 661 removed outlier: 6.568A pdb=" N MET A 675 " --> pdb=" O ALA A 660 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.837A pdb=" N ASP A 172 " --> pdb=" O GLY A 234 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY A 234 " --> pdb=" O ASP A 172 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ARG A 174 " --> pdb=" O VAL A 232 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 232 " --> pdb=" O ARG A 174 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 182 through 184 removed outlier: 6.149A pdb=" N ASP A 184 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 223 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 592 through 594 removed outlier: 3.849A pdb=" N ALA A 615 " --> pdb=" O GLN A 592 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N VAL A 594 " --> pdb=" O ALA A 615 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE A 617 " --> pdb=" O VAL A 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= K 327 hydrogen bonds defined for protein. 963 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: 2.36 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1395 1.33 - 1.45: 1425 1.45 - 1.57: 4070 1.57 - 1.69: 5 1.69 - 1.81: 86 Bond restraints: 6981 Sorted by residual: bond pdb=" O3A ACP A1003 " pdb=" PB ACP A1003 " ideal model delta sigma weight residual 1.698 1.578 0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" C3B ACP A1003 " pdb=" PG ACP A1003 " ideal model delta sigma weight residual 1.875 1.785 0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" CA THR A 352 " pdb=" C THR A 352 " ideal model delta sigma weight residual 1.526 1.470 0.057 1.35e-02 5.49e+03 1.76e+01 bond pdb=" O5' ACP A1003 " pdb=" PA ACP A1003 " ideal model delta sigma weight residual 1.659 1.581 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" O1G ACP A1003 " pdb=" PG ACP A1003 " ideal model delta sigma weight residual 1.533 1.459 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 6976 not shown) Histogram of bond angle deviations from ideal: 93.03 - 101.53: 35 101.53 - 110.03: 862 110.03 - 118.53: 4878 118.53 - 127.04: 3626 127.04 - 135.54: 59 Bond angle restraints: 9460 Sorted by residual: angle pdb=" N PRO A 201 " pdb=" CD PRO A 201 " pdb=" CG PRO A 201 " ideal model delta sigma weight residual 103.20 95.23 7.97 1.50e+00 4.44e-01 2.82e+01 angle pdb=" CA PRO A 201 " pdb=" CB PRO A 201 " pdb=" CG PRO A 201 " ideal model delta sigma weight residual 104.50 94.66 9.84 1.90e+00 2.77e-01 2.68e+01 angle pdb=" CA PRO A 201 " pdb=" N PRO A 201 " pdb=" CD PRO A 201 " ideal model delta sigma weight residual 112.00 105.98 6.02 1.40e+00 5.10e-01 1.85e+01 angle pdb=" CB PRO A 201 " pdb=" CG PRO A 201 " pdb=" CD PRO A 201 " ideal model delta sigma weight residual 106.10 93.03 13.07 3.20e+00 9.77e-02 1.67e+01 angle pdb=" O1B ACP A1003 " pdb=" PB ACP A1003 " pdb=" O2B ACP A1003 " ideal model delta sigma weight residual 119.60 108.46 11.14 3.00e+00 1.11e-01 1.38e+01 ... (remaining 9455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.74: 3654 19.74 - 39.49: 508 39.49 - 59.23: 98 59.23 - 78.98: 11 78.98 - 98.72: 8 Dihedral angle restraints: 4279 sinusoidal: 1707 harmonic: 2572 Sorted by residual: dihedral pdb=" O1A ACP A1003 " pdb=" O3A ACP A1003 " pdb=" PA ACP A1003 " pdb=" PB ACP A1003 " ideal model delta sinusoidal sigma weight residual -48.75 49.97 -98.72 1 3.00e+01 1.11e-03 1.23e+01 dihedral pdb=" CA GLU A 129 " pdb=" C GLU A 129 " pdb=" N GLU A 130 " pdb=" CA GLU A 130 " ideal model delta harmonic sigma weight residual 180.00 163.01 16.99 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASN A 822 " pdb=" CB ASN A 822 " pdb=" CG ASN A 822 " pdb=" OD1 ASN A 822 " ideal model delta sinusoidal sigma weight residual -90.00 -159.44 69.44 2 2.00e+01 2.50e-03 1.05e+01 ... (remaining 4276 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 843 0.040 - 0.079: 206 0.079 - 0.119: 78 0.119 - 0.158: 5 0.158 - 0.198: 3 Chirality restraints: 1135 Sorted by residual: chirality pdb=" C2' ACP A1003 " pdb=" C1' ACP A1003 " pdb=" C3' ACP A1003 " pdb=" O2' ACP A1003 " both_signs ideal model delta sigma weight residual False -2.75 -2.55 -0.20 2.00e-01 2.50e+01 9.80e-01 chirality pdb=" CB ILE A 894 " pdb=" CA ILE A 894 " pdb=" CG1 ILE A 894 " pdb=" CG2 ILE A 894 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.07e-01 chirality pdb=" CA THR A 354 " pdb=" N THR A 354 " pdb=" C THR A 354 " pdb=" CB THR A 354 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.96e-01 ... (remaining 1132 not shown) Planarity restraints: 1190 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 136 " -0.038 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO A 137 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 137 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 137 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 72 " 0.012 2.00e-02 2.50e+03 1.29e-02 4.17e+00 pdb=" CG TRP A 72 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 72 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 72 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 72 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 72 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 72 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 72 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 861 " -0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO A 862 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 862 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 862 " -0.027 5.00e-02 4.00e+02 ... (remaining 1187 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 190 2.70 - 3.25: 6797 3.25 - 3.80: 10952 3.80 - 4.35: 13215 4.35 - 4.90: 22297 Nonbonded interactions: 53451 Sorted by model distance: nonbonded pdb="MG MG A1002 " pdb=" O1G ACP A1003 " model vdw 2.149 2.170 nonbonded pdb=" OD1 ASN A 701 " pdb=" NE2 GLN A 829 " model vdw 2.206 2.520 nonbonded pdb=" O ILE A 836 " pdb=" OG SER A 840 " model vdw 2.263 2.440 nonbonded pdb=" O PHE A 861 " pdb=" N GLN A 865 " model vdw 2.281 2.520 nonbonded pdb=" NE2 GLN A 865 " pdb=" O GLU A 871 " model vdw 2.285 2.520 ... (remaining 53446 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: 2.250 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: 0.010 Extract box with map and model: 11.020 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 23.700 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 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 0.120 6981 Z= 0.293 Angle : 0.701 13.074 9460 Z= 0.343 Chirality : 0.040 0.198 1135 Planarity : 0.004 0.056 1190 Dihedral : 18.077 98.719 2615 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.26 % Allowed : 30.73 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 891 helix: 2.07 (0.24), residues: 465 sheet: -1.15 (0.72), residues: 67 loop : -1.09 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 72 HIS 0.002 0.000 HIS A 149 PHE 0.017 0.001 PHE A 118 TYR 0.003 0.000 TYR A 696 ARG 0.006 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7222 (mmmt) REVERT: A 264 LEU cc_start: 0.7846 (tt) cc_final: 0.7517 (tp) outliers start: 2 outliers final: 1 residues processed: 140 average time/residue: 0.2162 time to fit residues: 42.2449 Evaluate side-chains 130 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 51 optimal weight: 6.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6981 Z= 0.194 Angle : 0.541 6.582 9460 Z= 0.276 Chirality : 0.041 0.151 1135 Planarity : 0.004 0.044 1190 Dihedral : 6.563 69.681 974 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.65 % Allowed : 28.39 % Favored : 67.97 % 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: 0.90 (0.29), residues: 891 helix: 2.10 (0.24), residues: 459 sheet: -1.47 (0.58), residues: 87 loop : -0.92 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 72 HIS 0.003 0.001 HIS A 140 PHE 0.008 0.001 PHE A 844 TYR 0.013 0.001 TYR A 618 ARG 0.003 0.000 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 ARG cc_start: 0.8380 (ptm160) cc_final: 0.8146 (ptm160) REVERT: A 264 LEU cc_start: 0.7968 (tt) cc_final: 0.7615 (tp) REVERT: A 794 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7145 (m-80) outliers start: 28 outliers final: 13 residues processed: 162 average time/residue: 0.1968 time to fit residues: 42.9661 Evaluate side-chains 145 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 766 TRP Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 ASN A 140 HIS ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6981 Z= 0.210 Angle : 0.541 8.236 9460 Z= 0.276 Chirality : 0.041 0.171 1135 Planarity : 0.004 0.043 1190 Dihedral : 6.160 51.978 973 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.43 % Allowed : 27.99 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.29), residues: 891 helix: 1.98 (0.24), residues: 459 sheet: -1.51 (0.58), residues: 87 loop : -0.87 (0.33), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 72 HIS 0.004 0.001 HIS A 624 PHE 0.018 0.001 PHE A 118 TYR 0.011 0.001 TYR A 618 ARG 0.006 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7537 (tp30) cc_final: 0.7077 (tp30) REVERT: A 37 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7874 (mt) REVERT: A 153 ARG cc_start: 0.8446 (ptm160) cc_final: 0.8210 (ptm160) REVERT: A 264 LEU cc_start: 0.7992 (tt) cc_final: 0.7684 (tp) REVERT: A 329 ARG cc_start: 0.7319 (mtm-85) cc_final: 0.7089 (mtm-85) REVERT: A 381 ASN cc_start: 0.7105 (p0) cc_final: 0.6872 (p0) REVERT: A 742 ASP cc_start: 0.8020 (p0) cc_final: 0.7660 (p0) REVERT: A 748 SER cc_start: 0.8926 (m) cc_final: 0.8518 (m) REVERT: A 794 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.7311 (m-80) outliers start: 34 outliers final: 17 residues processed: 160 average time/residue: 0.1904 time to fit residues: 41.4185 Evaluate side-chains 144 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 TRP Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 0.0030 chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 GLN A 605 GLN ** A 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6981 Z= 0.173 Angle : 0.514 6.262 9460 Z= 0.262 Chirality : 0.040 0.145 1135 Planarity : 0.004 0.045 1190 Dihedral : 5.933 49.526 973 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 4.04 % Allowed : 28.39 % Favored : 67.58 % 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: 0.88 (0.29), residues: 891 helix: 2.05 (0.24), residues: 459 sheet: -1.61 (0.55), residues: 93 loop : -0.82 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 72 HIS 0.002 0.000 HIS A 149 PHE 0.018 0.001 PHE A 725 TYR 0.010 0.001 TYR A 618 ARG 0.003 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.854 Fit side-chains revert: symmetry clash REVERT: A 37 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8062 (mt) REVERT: A 264 LEU cc_start: 0.7955 (tt) cc_final: 0.7634 (tp) REVERT: A 271 PHE cc_start: 0.7300 (m-10) cc_final: 0.7041 (m-80) REVERT: A 381 ASN cc_start: 0.7189 (p0) cc_final: 0.6964 (p0) REVERT: A 437 MET cc_start: 0.8306 (mmm) cc_final: 0.8097 (tpp) REVERT: A 691 GLU cc_start: 0.5860 (OUTLIER) cc_final: 0.5585 (mp0) REVERT: A 717 ILE cc_start: 0.6746 (mm) cc_final: 0.6210 (mm) REVERT: A 748 SER cc_start: 0.8906 (m) cc_final: 0.8617 (m) REVERT: A 794 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7397 (m-80) outliers start: 31 outliers final: 23 residues processed: 154 average time/residue: 0.1896 time to fit residues: 39.0086 Evaluate side-chains 152 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 388 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 TRP Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 35 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 59 optimal weight: 0.0370 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 GLN ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6981 Z= 0.155 Angle : 0.514 6.151 9460 Z= 0.262 Chirality : 0.040 0.139 1135 Planarity : 0.004 0.047 1190 Dihedral : 5.786 48.136 973 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 4.30 % Allowed : 28.78 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 891 helix: 2.07 (0.24), residues: 461 sheet: -1.61 (0.55), residues: 93 loop : -0.82 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 72 HIS 0.002 0.000 HIS A 149 PHE 0.018 0.001 PHE A 725 TYR 0.009 0.001 TYR A 618 ARG 0.004 0.000 ARG A 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 GLU cc_start: 0.7556 (tp30) cc_final: 0.7288 (tp30) REVERT: A 37 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7571 (mt) REVERT: A 264 LEU cc_start: 0.7932 (tt) cc_final: 0.7636 (tp) REVERT: A 271 PHE cc_start: 0.7251 (m-10) cc_final: 0.6998 (m-80) REVERT: A 381 ASN cc_start: 0.7234 (p0) cc_final: 0.6967 (p0) REVERT: A 382 GLN cc_start: 0.6579 (tp40) cc_final: 0.6298 (pm20) REVERT: A 437 MET cc_start: 0.8356 (mmm) cc_final: 0.8136 (tpp) REVERT: A 748 SER cc_start: 0.8840 (m) cc_final: 0.8574 (m) REVERT: A 773 LYS cc_start: 0.7183 (OUTLIER) cc_final: 0.6930 (mtmt) outliers start: 33 outliers final: 23 residues processed: 158 average time/residue: 0.1910 time to fit residues: 40.1766 Evaluate side-chains 151 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 719 LEU Chi-restraints excluded: chain A residue 766 TRP Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 215 ASN ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6981 Z= 0.295 Angle : 0.628 8.264 9460 Z= 0.322 Chirality : 0.044 0.234 1135 Planarity : 0.004 0.047 1190 Dihedral : 6.130 47.541 973 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 5.34 % Allowed : 29.04 % Favored : 65.62 % 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: 0.32 (0.29), residues: 891 helix: 1.54 (0.24), residues: 460 sheet: -1.87 (0.54), residues: 93 loop : -0.99 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 60 HIS 0.002 0.001 HIS A 140 PHE 0.021 0.002 PHE A 725 TYR 0.033 0.002 TYR A 618 ARG 0.004 0.001 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 137 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6916 (tm-30) REVERT: A 264 LEU cc_start: 0.7954 (tt) cc_final: 0.7694 (tp) REVERT: A 274 PHE cc_start: 0.8480 (m-80) cc_final: 0.8108 (m-10) REVERT: A 308 GLU cc_start: 0.8313 (pm20) cc_final: 0.7674 (pm20) REVERT: A 505 GLN cc_start: 0.7899 (pp30) cc_final: 0.7263 (pp30) REVERT: A 513 GLU cc_start: 0.7966 (tp30) cc_final: 0.7695 (tp30) REVERT: A 671 GLU cc_start: 0.7559 (mt-10) cc_final: 0.7313 (mt-10) REVERT: A 742 ASP cc_start: 0.8057 (p0) cc_final: 0.7827 (p0) REVERT: A 794 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.7584 (m-80) outliers start: 41 outliers final: 28 residues processed: 164 average time/residue: 0.1932 time to fit residues: 42.7004 Evaluate side-chains 159 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 766 TRP Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 794 PHE Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 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 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6981 Z= 0.232 Angle : 0.595 10.879 9460 Z= 0.301 Chirality : 0.042 0.218 1135 Planarity : 0.004 0.048 1190 Dihedral : 6.077 46.596 973 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 5.34 % Allowed : 30.21 % Favored : 64.45 % 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: 0.32 (0.29), residues: 891 helix: 1.56 (0.24), residues: 464 sheet: -1.90 (0.54), residues: 93 loop : -1.04 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 285 HIS 0.002 0.001 HIS A 58 PHE 0.017 0.001 PHE A 725 TYR 0.012 0.001 TYR A 618 ARG 0.004 0.000 ARG A 213 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 134 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6864 (tm-30) REVERT: A 215 ASN cc_start: 0.5521 (OUTLIER) cc_final: 0.5313 (p0) REVERT: A 264 LEU cc_start: 0.7989 (tt) cc_final: 0.7714 (tp) REVERT: A 274 PHE cc_start: 0.8473 (m-80) cc_final: 0.8003 (m-10) REVERT: A 308 GLU cc_start: 0.8307 (pm20) cc_final: 0.7735 (pm20) REVERT: A 505 GLN cc_start: 0.7865 (pp30) cc_final: 0.7662 (pp30) REVERT: A 671 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 773 LYS cc_start: 0.7479 (OUTLIER) cc_final: 0.7206 (mtmt) outliers start: 41 outliers final: 27 residues processed: 161 average time/residue: 0.1923 time to fit residues: 41.1419 Evaluate side-chains 160 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 215 ASN Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 766 TRP Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 765 ASN ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6981 Z= 0.247 Angle : 0.607 9.329 9460 Z= 0.311 Chirality : 0.043 0.217 1135 Planarity : 0.004 0.049 1190 Dihedral : 6.055 45.125 973 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.69 % Allowed : 30.08 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.29), residues: 891 helix: 1.53 (0.24), residues: 463 sheet: -1.57 (0.55), residues: 99 loop : -1.23 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 60 HIS 0.002 0.001 HIS A 58 PHE 0.026 0.002 PHE A 118 TYR 0.022 0.001 TYR A 618 ARG 0.003 0.000 ARG A 842 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: A 227 LYS cc_start: 0.8437 (mmmt) cc_final: 0.7646 (mmmt) REVERT: A 264 LEU cc_start: 0.7948 (tt) cc_final: 0.7714 (tp) REVERT: A 308 GLU cc_start: 0.8397 (pm20) cc_final: 0.8053 (pm20) REVERT: A 505 GLN cc_start: 0.7885 (pp30) cc_final: 0.7684 (pp30) REVERT: A 671 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7362 (mt-10) REVERT: A 717 ILE cc_start: 0.7533 (mm) cc_final: 0.7225 (mm) outliers start: 36 outliers final: 30 residues processed: 156 average time/residue: 0.1893 time to fit residues: 39.3566 Evaluate side-chains 159 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 491 THR Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 707 LEU Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 75 optimal weight: 0.3980 chunk 79 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 84 optimal weight: 0.6980 chunk 51 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS A 419 ASN ** A 505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6981 Z= 0.208 Angle : 0.612 12.559 9460 Z= 0.307 Chirality : 0.042 0.211 1135 Planarity : 0.004 0.050 1190 Dihedral : 5.976 45.134 973 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 4.30 % Allowed : 30.86 % Favored : 64.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.29), residues: 891 helix: 1.60 (0.24), residues: 464 sheet: -1.61 (0.54), residues: 99 loop : -1.19 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 795 HIS 0.002 0.000 HIS A 58 PHE 0.025 0.001 PHE A 118 TYR 0.021 0.001 TYR A 618 ARG 0.002 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 0.819 Fit side-chains revert: symmetry clash REVERT: A 148 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6845 (tm-30) REVERT: A 227 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7603 (mmmt) REVERT: A 264 LEU cc_start: 0.7937 (tt) cc_final: 0.7723 (tp) REVERT: A 308 GLU cc_start: 0.8335 (pm20) cc_final: 0.8048 (pm20) REVERT: A 671 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7340 (mt-10) REVERT: A 717 ILE cc_start: 0.7494 (mm) cc_final: 0.7209 (mm) REVERT: A 773 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7155 (mtmt) outliers start: 33 outliers final: 27 residues processed: 148 average time/residue: 0.2025 time to fit residues: 39.8523 Evaluate side-chains 153 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 741 MET Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 777 LEU Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 70 optimal weight: 0.0170 chunk 7 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 43 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6981 Z= 0.205 Angle : 0.591 8.072 9460 Z= 0.299 Chirality : 0.042 0.209 1135 Planarity : 0.004 0.051 1190 Dihedral : 5.919 45.176 973 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.17 % Allowed : 31.25 % Favored : 64.58 % 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: 0.37 (0.29), residues: 891 helix: 1.61 (0.24), residues: 465 sheet: -1.59 (0.54), residues: 99 loop : -1.13 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 766 HIS 0.002 0.000 HIS A 58 PHE 0.025 0.001 PHE A 118 TYR 0.020 0.001 TYR A 618 ARG 0.002 0.000 ARG A 549 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1782 Ramachandran restraints generated. 891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 0.727 Fit side-chains revert: symmetry clash REVERT: A 21 LEU cc_start: 0.7909 (tp) cc_final: 0.7669 (tp) REVERT: A 130 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6463 (mm-30) REVERT: A 148 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.6850 (tm-30) REVERT: A 227 LYS cc_start: 0.8403 (mmmt) cc_final: 0.7715 (mmmt) REVERT: A 264 LEU cc_start: 0.7922 (tt) cc_final: 0.7711 (tp) REVERT: A 661 MET cc_start: 0.8868 (mmt) cc_final: 0.8425 (mmt) REVERT: A 671 GLU cc_start: 0.7594 (mt-10) cc_final: 0.7348 (mt-10) REVERT: A 717 ILE cc_start: 0.7514 (mm) cc_final: 0.7223 (mm) outliers start: 32 outliers final: 26 residues processed: 146 average time/residue: 0.2053 time to fit residues: 39.1560 Evaluate side-chains 151 residues out of total 768 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 124 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 85 MET Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 296 THR Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 361 THR Chi-restraints excluded: chain A residue 369 ASP Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 623 ARG Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 647 ASN Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 678 VAL Chi-restraints excluded: chain A residue 680 ASP Chi-restraints excluded: chain A residue 830 THR Chi-restraints excluded: chain A residue 870 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.0070 chunk 80 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 140 HIS ** A 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN ** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.181840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148353 restraints weight = 9018.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.151441 restraints weight = 6194.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.153532 restraints weight = 4833.403| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6981 Z= 0.198 Angle : 0.623 12.693 9460 Z= 0.312 Chirality : 0.042 0.207 1135 Planarity : 0.004 0.050 1190 Dihedral : 5.875 45.267 973 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.56 % Allowed : 30.86 % Favored : 64.58 % 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: 0.45 (0.29), residues: 891 helix: 1.65 (0.24), residues: 467 sheet: -1.56 (0.54), residues: 99 loop : -1.07 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 766 HIS 0.002 0.000 HIS A 58 PHE 0.025 0.001 PHE A 118 TYR 0.016 0.001 TYR A 618 ARG 0.002 0.000 ARG A 448 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.76 seconds wall clock time: 34 minutes 36.67 seconds (2076.67 seconds total)