Starting phenix.real_space_refine on Sat Dec 28 16:50:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bw7_30229/12_2024/7bw7_30229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bw7_30229/12_2024/7bw7_30229.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7bw7_30229/12_2024/7bw7_30229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bw7_30229/12_2024/7bw7_30229.map" model { file = "/net/cci-nas-00/data/ceres_data/7bw7_30229/12_2024/7bw7_30229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bw7_30229/12_2024/7bw7_30229.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 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 56 5.16 5 C 5621 2.51 5 N 1509 2.21 5 O 1638 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8824 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5224 Classifications: {'peptide': 647} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 613} Chain breaks: 5 Chain: "C" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3224 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 19, 'TRANS': 376} Chain breaks: 4 Chain: "D" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 376 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 1, 'TRANS': 46} Chain breaks: 1 Time building chain proxies: 5.15, per 1000 atoms: 0.58 Number of scatterers: 8824 At special positions: 0 Unit cell: (91.79, 108.23, 153.44, 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 56 16.00 O 1638 8.00 N 1509 7.00 C 5621 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.02 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.04 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A 435 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS A 786 " - pdb=" SG CYS A 795 " distance=2.03 Simple disulfide: pdb=" SG CYS C 786 " - pdb=" SG CYS C 795 " distance=2.03 Simple disulfide: pdb=" SG CYS D 7 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 19 " - pdb=" SG CYS D 75 " distance=2.04 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 66 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 989.0 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2068 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 14 sheets defined 13.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 16 through 20 removed outlier: 3.745A pdb=" N ARG A 19 " --> pdb=" O ASN A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.558A pdb=" N ASP A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.956A pdb=" N HIS A 199 " --> pdb=" O CYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 removed outlier: 3.854A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N CYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASN A 268 " --> pdb=" O HIS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.751A pdb=" N GLY A 317 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 318 " --> pdb=" O LEU A 315 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 314 through 318' Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 350 through 358 removed outlier: 3.515A pdb=" N LEU A 354 " --> pdb=" O LEU A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.777A pdb=" N GLY A 447 " --> pdb=" O GLU A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 323 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 435 through 440 removed outlier: 4.208A pdb=" N ILE C 439 " --> pdb=" O CYS C 435 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N HIS C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 440' Processing helix chain 'C' and resid 440 through 445 Processing helix chain 'C' and resid 496 through 500 Processing helix chain 'C' and resid 692 through 710 removed outlier: 3.730A pdb=" N GLU C 698 " --> pdb=" O LYS C 694 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER C 700 " --> pdb=" O LEU C 696 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS C 703 " --> pdb=" O SER C 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 19 removed outlier: 3.824A pdb=" N CYS D 19 " --> pdb=" O LEU D 15 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14 removed outlier: 6.586A pdb=" N VAL A 66 " --> pdb=" O LEU A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 3.517A pdb=" N ILE A 82 " --> pdb=" O ASN A 111 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.816A pdb=" N ASN A 148 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 removed outlier: 3.736A pdb=" N VAL A 254 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE A 248 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 280 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.521A pdb=" N CYS A 312 " --> pdb=" O VAL A 335 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 480 removed outlier: 6.560A pdb=" N ARG A 488 " --> pdb=" O SER A 476 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 478 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU A 486 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 530 through 533 removed outlier: 3.948A pdb=" N THR A 530 " --> pdb=" O TYR A 507 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 507 " --> pdb=" O THR A 530 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL A 566 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASP A 584 " --> pdb=" O VAL A 566 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 599 through 602 removed outlier: 6.607A pdb=" N LYS A 614 " --> pdb=" O PRO A 601 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 318 through 321 removed outlier: 6.590A pdb=" N LYS C 319 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU C 340 " --> pdb=" O LYS C 369 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 531 through 533 removed outlier: 3.542A pdb=" N VAL C 532 " --> pdb=" O LEU C 505 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 599 through 605 removed outlier: 4.858A pdb=" N ASP C 600 " --> pdb=" O LYS C 616 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 630 through 631 removed outlier: 3.651A pdb=" N GLU C 782 " --> pdb=" O PHE C 631 " (cutoff:3.500A) 119 hydrogen bonds defined for protein. 279 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.94 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2764 1.34 - 1.46: 2073 1.46 - 1.58: 4125 1.58 - 1.71: 0 1.71 - 1.83: 70 Bond restraints: 9032 Sorted by residual: bond pdb=" C VAL C 597 " pdb=" N PRO C 598 " ideal model delta sigma weight residual 1.330 1.377 -0.047 1.25e-02 6.40e+03 1.41e+01 bond pdb=" CA LEU C 696 " pdb=" C LEU C 696 " ideal model delta sigma weight residual 1.522 1.457 0.064 1.72e-02 3.38e+03 1.39e+01 bond pdb=" N VAL A 377 " pdb=" CA VAL A 377 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.08e-02 8.57e+03 1.24e+01 bond pdb=" N GLY C 580 " pdb=" CA GLY C 580 " ideal model delta sigma weight residual 1.446 1.485 -0.039 1.13e-02 7.83e+03 1.19e+01 bond pdb=" N THR C 578 " pdb=" CA THR C 578 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 1.02e+01 ... (remaining 9027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11418 1.95 - 3.90: 687 3.90 - 5.86: 101 5.86 - 7.81: 18 7.81 - 9.76: 9 Bond angle restraints: 12233 Sorted by residual: angle pdb=" C TYR C 579 " pdb=" CA TYR C 579 " pdb=" CB TYR C 579 " ideal model delta sigma weight residual 110.04 100.28 9.76 1.51e+00 4.39e-01 4.18e+01 angle pdb=" N PRO C 621 " pdb=" CA PRO C 621 " pdb=" C PRO C 621 " ideal model delta sigma weight residual 113.86 106.93 6.93 1.25e+00 6.40e-01 3.07e+01 angle pdb=" N PRO A 432 " pdb=" CA PRO A 432 " pdb=" C PRO A 432 " ideal model delta sigma weight residual 113.40 120.78 -7.38 1.34e+00 5.57e-01 3.04e+01 angle pdb=" C VAL C 597 " pdb=" N PRO C 598 " pdb=" CA PRO C 598 " ideal model delta sigma weight residual 120.21 125.30 -5.09 9.60e-01 1.09e+00 2.81e+01 angle pdb=" N VAL A 324 " pdb=" CA VAL A 324 " pdb=" C VAL A 324 " ideal model delta sigma weight residual 111.89 104.50 7.39 1.44e+00 4.82e-01 2.64e+01 ... (remaining 12228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4697 17.95 - 35.90: 610 35.90 - 53.85: 129 53.85 - 71.80: 14 71.80 - 89.75: 9 Dihedral angle restraints: 5459 sinusoidal: 2267 harmonic: 3192 Sorted by residual: dihedral pdb=" CB CYS D 19 " pdb=" SG CYS D 19 " pdb=" SG CYS D 75 " pdb=" CB CYS D 75 " ideal model delta sinusoidal sigma weight residual -86.00 -151.20 65.20 1 1.00e+01 1.00e-02 5.57e+01 dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 237 " pdb=" CB CYS A 237 " ideal model delta sinusoidal sigma weight residual -86.00 -145.19 59.19 1 1.00e+01 1.00e-02 4.68e+01 dihedral pdb=" CA CYS A 207 " pdb=" C CYS A 207 " pdb=" N CYS A 208 " pdb=" CA CYS A 208 " ideal model delta harmonic sigma weight residual -180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 5456 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1020 0.067 - 0.133: 274 0.133 - 0.200: 39 0.200 - 0.266: 3 0.266 - 0.333: 1 Chirality restraints: 1337 Sorted by residual: chirality pdb=" CA PRO A 432 " pdb=" N PRO A 432 " pdb=" C PRO A 432 " pdb=" CB PRO A 432 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CG LEU C 434 " pdb=" CB LEU C 434 " pdb=" CD1 LEU C 434 " pdb=" CD2 LEU C 434 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE C 457 " pdb=" N ILE C 457 " pdb=" C ILE C 457 " pdb=" CB ILE C 457 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1334 not shown) Planarity restraints: 1568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 577 " -0.022 2.00e-02 2.50e+03 4.53e-02 2.05e+01 pdb=" C ARG C 577 " 0.078 2.00e-02 2.50e+03 pdb=" O ARG C 577 " -0.029 2.00e-02 2.50e+03 pdb=" N THR C 578 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 494 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO C 495 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 495 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 495 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 591 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.92e+00 pdb=" C ASP C 591 " -0.042 2.00e-02 2.50e+03 pdb=" O ASP C 591 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA C 592 " 0.015 2.00e-02 2.50e+03 ... (remaining 1565 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 245 2.62 - 3.19: 8823 3.19 - 3.76: 13629 3.76 - 4.33: 18090 4.33 - 4.90: 27791 Nonbonded interactions: 68578 Sorted by model distance: nonbonded pdb=" OG SER C 437 " pdb=" O GLU C 517 " model vdw 2.050 3.040 nonbonded pdb=" OG SER A 116 " pdb=" OD1 ASN A 143 " model vdw 2.118 3.040 nonbonded pdb=" OG SER A 198 " pdb=" NE ARG A 229 " model vdw 2.122 3.120 nonbonded pdb=" OH TYR A 628 " pdb=" OE2 GLU A 766 " model vdw 2.136 3.040 nonbonded pdb=" OG SER D 67 " pdb=" OE1 GLN D 70 " model vdw 2.141 3.040 ... (remaining 68573 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.210 Find NCS groups from input model: 0.070 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 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 : 0.008 0.078 9032 Z= 0.508 Angle : 1.056 9.759 12233 Z= 0.606 Chirality : 0.060 0.333 1337 Planarity : 0.006 0.066 1568 Dihedral : 16.200 89.747 3340 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 40.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.38 % Favored : 76.62 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -5.62 (0.21), residues: 1065 helix: -3.74 (0.35), residues: 101 sheet: -3.83 (0.34), residues: 190 loop : -4.03 (0.19), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 183 HIS 0.007 0.002 HIS D 5 PHE 0.029 0.003 PHE A 400 TYR 0.027 0.003 TYR D 26 ARG 0.009 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 1.006 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: A 101 LEU cc_start: 0.7987 (tt) cc_final: 0.7682 (tp) REVERT: A 246 TYR cc_start: 0.7658 (m-80) cc_final: 0.7110 (m-80) REVERT: A 382 PHE cc_start: 0.8574 (m-10) cc_final: 0.8320 (m-10) REVERT: A 513 GLN cc_start: 0.7419 (tp-100) cc_final: 0.6743 (mp10) REVERT: A 616 LYS cc_start: 0.9016 (tppt) cc_final: 0.8632 (tppt) REVERT: A 780 ARG cc_start: 0.7569 (ptt180) cc_final: 0.7125 (ptm-80) REVERT: C 355 GLU cc_start: 0.7858 (tt0) cc_final: 0.7392 (pt0) REVERT: C 382 PHE cc_start: 0.8463 (t80) cc_final: 0.7999 (t80) REVERT: C 552 LEU cc_start: 0.9076 (tp) cc_final: 0.8812 (tp) REVERT: C 780 ARG cc_start: 0.7148 (ttt-90) cc_final: 0.6133 (mtp85) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2970 time to fit residues: 60.3441 Evaluate side-chains 117 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 27 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 GLN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 711 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9032 Z= 0.332 Angle : 0.877 12.119 12233 Z= 0.449 Chirality : 0.052 0.173 1337 Planarity : 0.006 0.055 1568 Dihedral : 7.791 26.961 1184 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.72 % Favored : 80.28 % Rotamer: Outliers : 0.20 % Allowed : 13.72 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -5.36 (0.22), residues: 1065 helix: -3.40 (0.35), residues: 108 sheet: -3.84 (0.32), residues: 202 loop : -3.78 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 632 HIS 0.007 0.001 HIS A 429 PHE 0.023 0.002 PHE A 381 TYR 0.030 0.002 TYR A 430 ARG 0.007 0.001 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 156 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.6756 (mmm160) cc_final: 0.6117 (mmt180) REVERT: A 246 TYR cc_start: 0.7044 (m-80) cc_final: 0.6561 (m-80) REVERT: A 294 MET cc_start: 0.6154 (ppp) cc_final: 0.5899 (ppp) REVERT: A 355 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8216 (pp20) REVERT: A 425 LYS cc_start: 0.7267 (ttmt) cc_final: 0.6867 (tmtt) REVERT: A 426 LEU cc_start: 0.7609 (tt) cc_final: 0.6820 (tt) REVERT: A 472 LEU cc_start: 0.6699 (tp) cc_final: 0.6488 (pt) REVERT: A 513 GLN cc_start: 0.7364 (tp-100) cc_final: 0.6715 (mp10) REVERT: A 616 LYS cc_start: 0.8819 (tppt) cc_final: 0.8408 (tppt) REVERT: C 355 GLU cc_start: 0.7821 (tt0) cc_final: 0.7325 (pt0) REVERT: C 381 PHE cc_start: 0.8607 (p90) cc_final: 0.8099 (p90) REVERT: C 409 ARG cc_start: 0.6303 (mtt90) cc_final: 0.6083 (mmt90) REVERT: C 552 LEU cc_start: 0.9086 (tp) cc_final: 0.7972 (tp) REVERT: C 577 ARG cc_start: 0.6705 (tpt-90) cc_final: 0.6501 (tpt-90) REVERT: C 614 LYS cc_start: 0.8327 (ptpp) cc_final: 0.8098 (ptmt) REVERT: C 780 ARG cc_start: 0.7041 (ttt-90) cc_final: 0.6008 (mtp85) outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.2591 time to fit residues: 53.8864 Evaluate side-chains 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 90 ASN A 100 HIS ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 ASN A 594 ASN ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 711 ASN ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9032 Z= 0.249 Angle : 0.809 10.592 12233 Z= 0.415 Chirality : 0.051 0.200 1337 Planarity : 0.005 0.049 1568 Dihedral : 7.254 28.854 1184 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.77 % Favored : 84.23 % Rotamer: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.92 (0.22), residues: 1065 helix: -2.96 (0.39), residues: 109 sheet: -3.70 (0.34), residues: 186 loop : -3.46 (0.20), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 251 HIS 0.005 0.001 HIS C 429 PHE 0.015 0.002 PHE A 382 TYR 0.023 0.002 TYR A 60 ARG 0.006 0.001 ARG C 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.019 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: A 83 ARG cc_start: 0.6540 (mmm160) cc_final: 0.5873 (mmt180) REVERT: A 294 MET cc_start: 0.5939 (ppp) cc_final: 0.5730 (ppp) REVERT: A 344 ILE cc_start: 0.8793 (mm) cc_final: 0.8582 (mm) REVERT: A 513 GLN cc_start: 0.7344 (tp-100) cc_final: 0.6719 (mp10) REVERT: A 616 LYS cc_start: 0.8803 (tppt) cc_final: 0.8315 (tppt) REVERT: A 765 LYS cc_start: 0.8056 (mttp) cc_final: 0.7265 (mttm) REVERT: A 783 LEU cc_start: 0.9114 (tp) cc_final: 0.8906 (tp) REVERT: C 355 GLU cc_start: 0.7656 (tt0) cc_final: 0.7205 (pt0) REVERT: C 381 PHE cc_start: 0.8379 (p90) cc_final: 0.8020 (p90) REVERT: C 382 PHE cc_start: 0.8479 (t80) cc_final: 0.8054 (t80) REVERT: C 552 LEU cc_start: 0.8971 (tp) cc_final: 0.8705 (tp) REVERT: C 780 ARG cc_start: 0.6760 (ttt-90) cc_final: 0.6094 (mtp-110) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.2418 time to fit residues: 52.7278 Evaluate side-chains 119 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 chunk 103 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 GLN ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9032 Z= 0.308 Angle : 0.805 9.331 12233 Z= 0.415 Chirality : 0.051 0.191 1337 Planarity : 0.005 0.047 1568 Dihedral : 7.262 29.582 1184 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.87 % Favored : 81.13 % Rotamer: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.84 (0.22), residues: 1065 helix: -2.80 (0.40), residues: 114 sheet: -3.59 (0.33), residues: 186 loop : -3.43 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 529 HIS 0.006 0.001 HIS C 627 PHE 0.020 0.002 PHE A 381 TYR 0.026 0.002 TYR A 430 ARG 0.008 0.001 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 1.042 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: A 83 ARG cc_start: 0.6606 (mmm160) cc_final: 0.5877 (mmt180) REVERT: A 98 MET cc_start: 0.6498 (mmp) cc_final: 0.6292 (mmm) REVERT: A 513 GLN cc_start: 0.7241 (tp-100) cc_final: 0.6558 (mp10) REVERT: A 616 LYS cc_start: 0.8775 (tppt) cc_final: 0.8359 (tppt) REVERT: A 765 LYS cc_start: 0.8017 (mttp) cc_final: 0.7182 (mttm) REVERT: A 783 LEU cc_start: 0.9123 (tp) cc_final: 0.8314 (tp) REVERT: C 382 PHE cc_start: 0.8342 (t80) cc_final: 0.8064 (t80) REVERT: C 552 LEU cc_start: 0.9105 (tp) cc_final: 0.8734 (tp) REVERT: C 577 ARG cc_start: 0.6565 (tpt-90) cc_final: 0.6191 (mmt180) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2332 time to fit residues: 47.5437 Evaluate side-chains 109 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 88 optimal weight: 0.0970 chunk 71 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.1980 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 overall best weight: 3.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9032 Z= 0.347 Angle : 0.823 10.519 12233 Z= 0.426 Chirality : 0.051 0.233 1337 Planarity : 0.005 0.051 1568 Dihedral : 7.312 29.885 1184 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 21.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.12 % Favored : 81.88 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.86 (0.22), residues: 1065 helix: -2.88 (0.40), residues: 119 sheet: -3.44 (0.34), residues: 191 loop : -3.48 (0.20), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 489 HIS 0.010 0.001 HIS D 5 PHE 0.023 0.003 PHE C 475 TYR 0.026 0.002 TYR A 401 ARG 0.010 0.001 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.033 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: A 83 ARG cc_start: 0.6636 (mmm160) cc_final: 0.5992 (mmt180) REVERT: A 110 MET cc_start: 0.7517 (mmp) cc_final: 0.6996 (mmm) REVERT: A 246 TYR cc_start: 0.7143 (m-80) cc_final: 0.6729 (m-80) REVERT: A 360 LEU cc_start: 0.7720 (mm) cc_final: 0.6953 (tt) REVERT: A 425 LYS cc_start: 0.7291 (ttmt) cc_final: 0.6801 (tmtt) REVERT: A 513 GLN cc_start: 0.7204 (tp-100) cc_final: 0.6552 (mp10) REVERT: A 616 LYS cc_start: 0.8890 (tttp) cc_final: 0.8600 (tppt) REVERT: A 765 LYS cc_start: 0.7886 (mttp) cc_final: 0.7132 (mttm) REVERT: A 783 LEU cc_start: 0.8873 (tp) cc_final: 0.8578 (tp) REVERT: C 382 PHE cc_start: 0.7983 (t80) cc_final: 0.7750 (t80) REVERT: C 518 PHE cc_start: 0.7552 (t80) cc_final: 0.6851 (t80) REVERT: C 552 LEU cc_start: 0.9216 (tp) cc_final: 0.8858 (tp) REVERT: C 780 ARG cc_start: 0.6708 (ttt-90) cc_final: 0.5749 (mtp85) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2332 time to fit residues: 44.2394 Evaluate side-chains 113 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 0.1980 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 0.2980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9032 Z= 0.210 Angle : 0.745 11.545 12233 Z= 0.379 Chirality : 0.049 0.155 1337 Planarity : 0.005 0.064 1568 Dihedral : 6.710 28.076 1184 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.47 (0.23), residues: 1065 helix: -2.67 (0.43), residues: 112 sheet: -3.43 (0.36), residues: 159 loop : -3.16 (0.20), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 412 HIS 0.005 0.001 HIS A 429 PHE 0.025 0.002 PHE A 631 TYR 0.027 0.002 TYR A 374 ARG 0.004 0.000 ARG C 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.968 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: A 11 MET cc_start: 0.5849 (mpp) cc_final: 0.5213 (tpt) REVERT: A 83 ARG cc_start: 0.6559 (mmm160) cc_final: 0.6119 (mmt180) REVERT: A 98 MET cc_start: 0.6422 (mmm) cc_final: 0.5964 (mmm) REVERT: A 246 TYR cc_start: 0.7720 (m-80) cc_final: 0.7415 (m-80) REVERT: A 360 LEU cc_start: 0.7526 (mm) cc_final: 0.6911 (tt) REVERT: A 401 TYR cc_start: 0.8366 (t80) cc_final: 0.8105 (t80) REVERT: A 513 GLN cc_start: 0.7283 (tp-100) cc_final: 0.6587 (mp10) REVERT: A 616 LYS cc_start: 0.8862 (tttp) cc_final: 0.8542 (tppt) REVERT: A 765 LYS cc_start: 0.7470 (mttp) cc_final: 0.6813 (mttm) REVERT: A 783 LEU cc_start: 0.8707 (tp) cc_final: 0.8348 (mt) REVERT: C 552 LEU cc_start: 0.9138 (tp) cc_final: 0.8875 (tp) REVERT: C 780 ARG cc_start: 0.6668 (ttt-90) cc_final: 0.5746 (mtp85) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2541 time to fit residues: 53.4777 Evaluate side-chains 125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9032 Z= 0.329 Angle : 0.809 9.595 12233 Z= 0.415 Chirality : 0.050 0.195 1337 Planarity : 0.005 0.050 1568 Dihedral : 7.042 29.080 1184 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 21.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.18 % Favored : 82.82 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.49 (0.23), residues: 1065 helix: -2.78 (0.43), residues: 110 sheet: -3.13 (0.35), residues: 188 loop : -3.21 (0.20), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 615 HIS 0.013 0.001 HIS A 429 PHE 0.031 0.003 PHE A 89 TYR 0.025 0.002 TYR A 430 ARG 0.007 0.001 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.5954 (mpp) cc_final: 0.5224 (tpt) REVERT: A 83 ARG cc_start: 0.6844 (mmm160) cc_final: 0.6144 (mmt180) REVERT: A 110 MET cc_start: 0.7507 (mmp) cc_final: 0.7182 (mmm) REVERT: A 360 LEU cc_start: 0.7510 (mm) cc_final: 0.6798 (tt) REVERT: A 425 LYS cc_start: 0.7257 (ttmt) cc_final: 0.6760 (tmtt) REVERT: A 513 GLN cc_start: 0.7327 (tp-100) cc_final: 0.6596 (mp10) REVERT: A 616 LYS cc_start: 0.8838 (tttp) cc_final: 0.8597 (tppt) REVERT: A 765 LYS cc_start: 0.7709 (mttp) cc_final: 0.6975 (mttm) REVERT: C 382 PHE cc_start: 0.8068 (t80) cc_final: 0.7715 (t80) REVERT: C 518 PHE cc_start: 0.7506 (t80) cc_final: 0.7190 (t80) REVERT: C 552 LEU cc_start: 0.9235 (tp) cc_final: 0.8887 (tp) REVERT: C 780 ARG cc_start: 0.6670 (ttt-90) cc_final: 0.5644 (mtp85) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2386 time to fit residues: 48.1124 Evaluate side-chains 110 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 9.9990 chunk 31 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 HIS C 407 ASN ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9032 Z= 0.198 Angle : 0.731 11.392 12233 Z= 0.370 Chirality : 0.048 0.180 1337 Planarity : 0.005 0.048 1568 Dihedral : 6.505 28.200 1184 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.12 (0.23), residues: 1065 helix: -2.65 (0.43), residues: 112 sheet: -3.08 (0.39), residues: 152 loop : -2.91 (0.20), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 632 HIS 0.012 0.001 HIS A 429 PHE 0.020 0.002 PHE A 631 TYR 0.026 0.002 TYR A 374 ARG 0.005 0.000 ARG A 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.5890 (mpp) cc_final: 0.5494 (tpt) REVERT: A 83 ARG cc_start: 0.6707 (mmm160) cc_final: 0.5945 (mmt180) REVERT: A 100 HIS cc_start: 0.6300 (m-70) cc_final: 0.6053 (m-70) REVERT: A 329 GLU cc_start: 0.6927 (mp0) cc_final: 0.6724 (mm-30) REVERT: A 360 LEU cc_start: 0.7607 (mm) cc_final: 0.6984 (tt) REVERT: A 504 MET cc_start: 0.4331 (mmm) cc_final: 0.3636 (mmm) REVERT: A 513 GLN cc_start: 0.7238 (tp-100) cc_final: 0.6483 (mp10) REVERT: A 518 PHE cc_start: 0.6628 (t80) cc_final: 0.6382 (t80) REVERT: A 616 LYS cc_start: 0.8743 (tttp) cc_final: 0.8492 (tppt) REVERT: A 765 LYS cc_start: 0.7444 (mttp) cc_final: 0.6760 (mttm) REVERT: A 783 LEU cc_start: 0.8880 (tp) cc_final: 0.8568 (mt) REVERT: C 518 PHE cc_start: 0.7397 (t80) cc_final: 0.7184 (t80) REVERT: C 552 LEU cc_start: 0.9082 (tp) cc_final: 0.8832 (tp) REVERT: C 700 SER cc_start: 0.8389 (m) cc_final: 0.8163 (t) REVERT: C 780 ARG cc_start: 0.6634 (ttt-90) cc_final: 0.5702 (mtp85) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2390 time to fit residues: 50.1307 Evaluate side-chains 124 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 7.9990 chunk 96 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 594 ASN ** C 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9032 Z= 0.352 Angle : 0.834 11.432 12233 Z= 0.427 Chirality : 0.052 0.196 1337 Planarity : 0.006 0.049 1568 Dihedral : 7.014 28.463 1184 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 17.75 % Favored : 82.16 % Rotamer: Outliers : 0.20 % Allowed : 0.50 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.34 (0.23), residues: 1065 helix: -2.74 (0.42), residues: 115 sheet: -3.06 (0.36), residues: 181 loop : -3.09 (0.21), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 412 HIS 0.008 0.001 HIS A 429 PHE 0.027 0.003 PHE A 89 TYR 0.030 0.002 TYR A 430 ARG 0.009 0.001 ARG A 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.5899 (mpp) cc_final: 0.5433 (tpt) REVERT: A 83 ARG cc_start: 0.6838 (mmm160) cc_final: 0.6059 (mmt180) REVERT: A 90 ASN cc_start: 0.7559 (p0) cc_final: 0.7229 (p0) REVERT: A 100 HIS cc_start: 0.6495 (m-70) cc_final: 0.6239 (m-70) REVERT: A 102 LYS cc_start: 0.6750 (pttp) cc_final: 0.6499 (pptt) REVERT: A 110 MET cc_start: 0.7540 (mmp) cc_final: 0.7158 (mmm) REVERT: A 147 LEU cc_start: 0.6517 (mp) cc_final: 0.6166 (mt) REVERT: A 404 ASP cc_start: 0.8667 (t0) cc_final: 0.8420 (t0) REVERT: A 513 GLN cc_start: 0.7348 (tp-100) cc_final: 0.6618 (mp10) REVERT: A 765 LYS cc_start: 0.7669 (mttp) cc_final: 0.6924 (mttm) REVERT: C 518 PHE cc_start: 0.7518 (t80) cc_final: 0.7239 (t80) REVERT: C 552 LEU cc_start: 0.9232 (tp) cc_final: 0.8874 (tp) REVERT: C 780 ARG cc_start: 0.6693 (ttt-90) cc_final: 0.5800 (mtp85) outliers start: 2 outliers final: 0 residues processed: 146 average time/residue: 0.2344 time to fit residues: 46.4509 Evaluate side-chains 107 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 106 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 9032 Z= 0.342 Angle : 0.827 10.707 12233 Z= 0.424 Chirality : 0.053 0.238 1337 Planarity : 0.005 0.057 1568 Dihedral : 7.078 28.215 1184 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.90 % Favored : 83.10 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.35 (0.23), residues: 1065 helix: -2.77 (0.41), residues: 116 sheet: -3.02 (0.36), residues: 181 loop : -3.10 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 412 HIS 0.006 0.001 HIS D 5 PHE 0.031 0.003 PHE A 96 TYR 0.021 0.002 TYR C 779 ARG 0.009 0.001 ARG A 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 MET cc_start: 0.5995 (mpp) cc_final: 0.5120 (tpt) REVERT: A 38 MET cc_start: 0.5262 (mmm) cc_final: 0.4870 (tpt) REVERT: A 83 ARG cc_start: 0.6807 (mmm160) cc_final: 0.6048 (mmt180) REVERT: A 90 ASN cc_start: 0.7418 (p0) cc_final: 0.7137 (p0) REVERT: A 100 HIS cc_start: 0.6468 (m-70) cc_final: 0.6225 (m-70) REVERT: A 102 LYS cc_start: 0.6665 (pttp) cc_final: 0.6461 (pptt) REVERT: A 110 MET cc_start: 0.7564 (mmp) cc_final: 0.7170 (mmm) REVERT: A 135 ARG cc_start: 0.7709 (mpt180) cc_final: 0.7250 (mpt180) REVERT: A 329 GLU cc_start: 0.7209 (mp0) cc_final: 0.6677 (mm-30) REVERT: A 404 ASP cc_start: 0.8623 (t0) cc_final: 0.8388 (t0) REVERT: A 513 GLN cc_start: 0.7248 (tp-100) cc_final: 0.6610 (mp10) REVERT: A 562 TYR cc_start: 0.7249 (m-10) cc_final: 0.7015 (m-10) REVERT: A 616 LYS cc_start: 0.9000 (tptp) cc_final: 0.8690 (tppt) REVERT: A 765 LYS cc_start: 0.7674 (mttp) cc_final: 0.6921 (mttm) REVERT: C 518 PHE cc_start: 0.7549 (t80) cc_final: 0.7205 (t80) REVERT: C 552 LEU cc_start: 0.9236 (tp) cc_final: 0.8910 (tp) REVERT: C 780 ARG cc_start: 0.6740 (ttt-90) cc_final: 0.5825 (mtp85) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2503 time to fit residues: 47.1195 Evaluate side-chains 111 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 74 optimal weight: 0.0970 chunk 4 optimal weight: 5.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 429 HIS ** 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 = 0.4856 r_free = 0.4856 target = 0.186832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.145259 restraints weight = 19086.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.146598 restraints weight = 15495.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.148022 restraints weight = 12154.913| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9032 Z= 0.232 Angle : 0.765 11.006 12233 Z= 0.388 Chirality : 0.050 0.257 1337 Planarity : 0.005 0.047 1568 Dihedral : 6.723 26.345 1184 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.46 % Favored : 85.54 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -4.11 (0.24), residues: 1065 helix: -2.61 (0.43), residues: 110 sheet: -3.01 (0.37), residues: 164 loop : -2.91 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 412 HIS 0.009 0.001 HIS A 429 PHE 0.019 0.002 PHE C 427 TYR 0.031 0.002 TYR A 374 ARG 0.008 0.001 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1939.66 seconds wall clock time: 36 minutes 22.09 seconds (2182.09 seconds total)