Starting phenix.real_space_refine on Thu Mar 13 10:29:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7bw7_30229/03_2025/7bw7_30229.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bw7_30229/03_2025/7bw7_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_30229/03_2025/7bw7_30229.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bw7_30229/03_2025/7bw7_30229.map" model { file = "/net/cci-nas-00/data/ceres_data/7bw7_30229/03_2025/7bw7_30229.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bw7_30229/03_2025/7bw7_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.99, per 1000 atoms: 0.57 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: 2.27 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.84 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: 1.96 Time building geometry restraints manager: 2.68 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: 0.200 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: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 21.700 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- 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 : 0.976 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: 0.3001 time to fit residues: 60.9880 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 : 0.989 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.181139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.140564 restraints weight = 19218.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.143202 restraints weight = 14436.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.145051 restraints weight = 11836.477| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 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 : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.6854 (mmm160) cc_final: 0.6185 (mmt180) REVERT: A 98 MET cc_start: 0.7495 (mmm) cc_final: 0.7294 (mmm) REVERT: A 246 TYR cc_start: 0.7049 (m-80) cc_final: 0.6562 (m-80) REVERT: A 294 MET cc_start: 0.6122 (ppp) cc_final: 0.5875 (ppp) REVERT: A 355 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8222 (pp20) REVERT: A 425 LYS cc_start: 0.7279 (ttmt) cc_final: 0.6902 (tmtt) REVERT: A 426 LEU cc_start: 0.7683 (tt) cc_final: 0.6926 (tt) REVERT: A 472 LEU cc_start: 0.6848 (tp) cc_final: 0.6624 (pt) REVERT: A 513 GLN cc_start: 0.7401 (tp-100) cc_final: 0.6757 (mp10) REVERT: A 616 LYS cc_start: 0.8846 (tppt) cc_final: 0.8423 (tppt) REVERT: C 355 GLU cc_start: 0.7974 (tt0) cc_final: 0.7410 (pt0) REVERT: C 381 PHE cc_start: 0.8746 (p90) cc_final: 0.8179 (p90) REVERT: C 382 PHE cc_start: 0.8534 (t80) cc_final: 0.8280 (t80) REVERT: C 409 ARG cc_start: 0.6245 (mtt90) cc_final: 0.6020 (mmt90) REVERT: C 552 LEU cc_start: 0.9145 (tp) cc_final: 0.8015 (tp) REVERT: C 780 ARG cc_start: 0.7012 (ttt-90) cc_final: 0.5951 (mtp85) outliers start: 2 outliers final: 1 residues processed: 157 average time/residue: 0.2573 time to fit residues: 53.5875 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 : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 59 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 25 optimal weight: 0.0270 chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 30.0000 chunk 15 optimal weight: 0.0870 chunk 46 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 overall best weight: 2.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 100 HIS ** 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 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 470 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.221327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.4818 r_free = 0.4818 target = 0.189984 restraints weight = 22318.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4847 r_free = 0.4847 target = 0.189396 restraints weight = 26569.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4842 r_free = 0.4842 target = 0.188856 restraints weight = 22570.140| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6453 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 9032 Z= 0.311 Angle : 0.845 10.078 12233 Z= 0.434 Chirality : 0.052 0.173 1337 Planarity : 0.005 0.052 1568 Dihedral : 7.549 29.630 1184 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.40 % Favored : 81.60 % Rotamer: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % 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: -5.07 (0.22), residues: 1065 helix: -3.21 (0.37), residues: 114 sheet: -3.73 (0.34), residues: 186 loop : -3.56 (0.19), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 251 HIS 0.006 0.001 HIS C 429 PHE 0.019 0.002 PHE A 382 TYR 0.027 0.002 TYR C 430 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 150 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.970 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: 0.6980 (mmm160) cc_final: 0.6286 (mmt180) REVERT: A 294 MET cc_start: 0.5759 (ppp) cc_final: 0.5481 (ppp) REVERT: A 427 PHE cc_start: 0.6960 (t80) cc_final: 0.6736 (t80) REVERT: A 513 GLN cc_start: 0.7313 (tp-100) cc_final: 0.6779 (mp10) REVERT: A 616 LYS cc_start: 0.8567 (tppt) cc_final: 0.8223 (tppt) REVERT: A 765 LYS cc_start: 0.7862 (mttp) cc_final: 0.7073 (mttm) REVERT: A 783 LEU cc_start: 0.9038 (tp) cc_final: 0.8463 (tp) REVERT: C 370 ILE cc_start: 0.8119 (mm) cc_final: 0.7843 (mm) REVERT: C 552 LEU cc_start: 0.9007 (tp) cc_final: 0.8697 (tp) REVERT: C 577 ARG cc_start: 0.6318 (tpt-90) cc_final: 0.6102 (mmt180) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2224 time to fit residues: 45.5900 Evaluate side-chains 116 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 15 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 93 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS ** 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** ** C 610 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 = 0.4842 r_free = 0.4842 target = 0.183609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.141003 restraints weight = 19186.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.143776 restraints weight = 14294.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.145626 restraints weight = 11820.147| |-----------------------------------------------------------------------------| r_work (final): 0.4318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9032 Z= 0.413 Angle : 0.893 10.757 12233 Z= 0.459 Chirality : 0.053 0.228 1337 Planarity : 0.006 0.056 1568 Dihedral : 7.810 30.095 1184 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 24.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.03 % Favored : 78.97 % Rotamer: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -5.19 (0.22), residues: 1065 helix: -3.23 (0.36), residues: 119 sheet: -3.62 (0.33), residues: 198 loop : -3.69 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 529 HIS 0.013 0.002 HIS D 5 PHE 0.030 0.003 PHE A 381 TYR 0.031 0.003 TYR A 401 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 138 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.6962 (mmm160) cc_final: 0.6238 (mmt180) REVERT: A 110 MET cc_start: 0.7896 (mmm) cc_final: 0.7647 (mmm) REVERT: A 120 GLU cc_start: 0.5536 (tt0) cc_final: 0.5332 (tt0) REVERT: A 425 LYS cc_start: 0.7366 (ttmt) cc_final: 0.6921 (tmtt) REVERT: A 481 SER cc_start: 0.8641 (m) cc_final: 0.8437 (p) REVERT: A 513 GLN cc_start: 0.7308 (tp-100) cc_final: 0.6612 (mp10) REVERT: A 616 LYS cc_start: 0.8879 (tppt) cc_final: 0.8466 (tppt) REVERT: A 765 LYS cc_start: 0.8083 (mttp) cc_final: 0.7253 (mttm) REVERT: C 518 PHE cc_start: 0.7799 (t80) cc_final: 0.7529 (t80) REVERT: C 552 LEU cc_start: 0.9128 (tp) cc_final: 0.8814 (tp) REVERT: C 577 ARG cc_start: 0.6453 (tpt-90) cc_final: 0.6237 (mmt90) REVERT: C 780 ARG cc_start: 0.6793 (ttt-90) cc_final: 0.5657 (mtp85) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2193 time to fit residues: 41.5689 Evaluate side-chains 106 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 10 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 9 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4990 r_free = 0.4990 target = 0.220497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.190803 restraints weight = 22062.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4846 r_free = 0.4846 target = 0.186145 restraints weight = 26824.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.187346 restraints weight = 22867.099| |-----------------------------------------------------------------------------| r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9032 Z= 0.303 Angle : 0.815 10.686 12233 Z= 0.420 Chirality : 0.052 0.203 1337 Planarity : 0.005 0.064 1568 Dihedral : 7.406 29.431 1184 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.03 % Favored : 81.97 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % 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: -4.96 (0.22), residues: 1065 helix: -3.22 (0.37), residues: 117 sheet: -3.56 (0.35), residues: 179 loop : -3.50 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 489 HIS 0.008 0.001 HIS D 5 PHE 0.022 0.002 PHE C 475 TYR 0.026 0.002 TYR A 374 ARG 0.006 0.001 ARG A 252 *********************** 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 147 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.964 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: 0.6733 (mmm160) cc_final: 0.6112 (mmt180) REVERT: A 110 MET cc_start: 0.7935 (mmm) cc_final: 0.7681 (mmm) REVERT: A 246 TYR cc_start: 0.7625 (m-80) cc_final: 0.7336 (m-80) REVERT: A 360 LEU cc_start: 0.7702 (mm) cc_final: 0.6994 (tt) REVERT: A 404 ASP cc_start: 0.8393 (t0) cc_final: 0.8092 (t0) REVERT: A 513 GLN cc_start: 0.7175 (tp-100) cc_final: 0.6628 (mp10) REVERT: A 616 LYS cc_start: 0.8540 (tppt) cc_final: 0.8192 (tppt) REVERT: A 764 ASN cc_start: 0.5755 (m-40) cc_final: 0.5555 (m-40) REVERT: A 765 LYS cc_start: 0.7540 (mttp) cc_final: 0.6900 (mttm) REVERT: C 552 LEU cc_start: 0.9021 (tp) cc_final: 0.8717 (tp) REVERT: C 780 ARG cc_start: 0.6855 (ttt-90) cc_final: 0.5963 (mtp85) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.2353 time to fit residues: 46.7083 Evaluate side-chains 114 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4988 r_free = 0.4988 target = 0.220041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.189232 restraints weight = 21850.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.185371 restraints weight = 26485.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.184294 restraints weight = 23440.421| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6525 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9032 Z= 0.328 Angle : 0.826 9.761 12233 Z= 0.423 Chirality : 0.051 0.180 1337 Planarity : 0.005 0.051 1568 Dihedral : 7.360 29.514 1184 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 20.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.31 % Favored : 81.69 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % 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: -4.87 (0.22), residues: 1065 helix: -3.16 (0.37), residues: 114 sheet: -3.45 (0.34), residues: 185 loop : -3.45 (0.20), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 489 HIS 0.007 0.001 HIS A 429 PHE 0.030 0.003 PHE C 475 TYR 0.050 0.003 TYR A 430 ARG 0.006 0.001 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 141 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.6983 (mmm) cc_final: 0.6770 (mmm) REVERT: A 100 HIS cc_start: 0.7307 (m-70) cc_final: 0.7035 (m-70) REVERT: A 110 MET cc_start: 0.7987 (mmm) cc_final: 0.7647 (mmm) REVERT: A 246 TYR cc_start: 0.7186 (m-80) cc_final: 0.6736 (m-80) REVERT: A 360 LEU cc_start: 0.7755 (mm) cc_final: 0.7016 (tt) REVERT: A 513 GLN cc_start: 0.7183 (tp-100) cc_final: 0.6657 (mp10) REVERT: A 765 LYS cc_start: 0.7310 (mttp) cc_final: 0.6663 (mttm) REVERT: C 382 PHE cc_start: 0.7538 (t80) cc_final: 0.7318 (t80) REVERT: C 552 LEU cc_start: 0.9177 (tp) cc_final: 0.8843 (tp) REVERT: C 695 GLU cc_start: 0.8633 (tp30) cc_final: 0.8256 (pm20) REVERT: C 780 ARG cc_start: 0.6903 (ttt-90) cc_final: 0.6056 (mtp85) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2192 time to fit residues: 42.2888 Evaluate side-chains 106 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 57 optimal weight: 0.0020 chunk 29 optimal weight: 0.8980 chunk 64 optimal weight: 0.1980 chunk 25 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 38 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 94 optimal weight: 0.0670 chunk 20 optimal weight: 0.4980 overall best weight: 0.2726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 337 ASN A 417 HIS A 429 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.229931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.201274 restraints weight = 22069.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4974 r_free = 0.4974 target = 0.199951 restraints weight = 25907.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.200514 restraints weight = 19548.876| |-----------------------------------------------------------------------------| r_work (final): 0.4584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9032 Z= 0.189 Angle : 0.748 12.531 12233 Z= 0.378 Chirality : 0.049 0.162 1337 Planarity : 0.005 0.049 1568 Dihedral : 6.612 29.228 1184 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: -4.23 (0.23), residues: 1065 helix: -2.74 (0.42), residues: 107 sheet: -2.93 (0.37), residues: 166 loop : -3.03 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 412 HIS 0.025 0.001 HIS A 429 PHE 0.020 0.002 PHE A 427 TYR 0.027 0.002 TYR D 74 ARG 0.010 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 159 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.039 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 11 MET cc_start: 0.6465 (mpp) cc_final: 0.5658 (tpt) REVERT: A 83 ARG cc_start: 0.6367 (mmm160) cc_final: 0.5981 (mmt180) REVERT: A 110 MET cc_start: 0.7782 (mmm) cc_final: 0.7345 (mmm) REVERT: A 144 TYR cc_start: 0.6575 (t80) cc_final: 0.6264 (t80) REVERT: A 294 MET cc_start: 0.5684 (ppp) cc_final: 0.5478 (ppp) REVERT: A 343 ASN cc_start: 0.7926 (t0) cc_final: 0.7717 (t0) REVERT: A 360 LEU cc_start: 0.7456 (mm) cc_final: 0.6905 (tt) REVERT: A 513 GLN cc_start: 0.7341 (tp-100) cc_final: 0.6700 (mp10) REVERT: A 616 LYS cc_start: 0.8563 (tptp) cc_final: 0.8276 (tppt) REVERT: A 765 LYS cc_start: 0.7136 (mttp) cc_final: 0.6606 (mttm) REVERT: A 783 LEU cc_start: 0.8459 (tp) cc_final: 0.8210 (mt) REVERT: C 552 LEU cc_start: 0.9025 (tp) cc_final: 0.8822 (tp) REVERT: C 700 SER cc_start: 0.8450 (m) cc_final: 0.8161 (t) REVERT: C 780 ARG cc_start: 0.6831 (ttt-90) cc_final: 0.6002 (mtp85) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2238 time to fit residues: 48.5240 Evaluate side-chains 122 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 83 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 32 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 71 optimal weight: 8.9990 chunk 58 optimal weight: 0.3980 chunk 74 optimal weight: 0.0980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN ** A 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 ASN ** C 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4904 r_free = 0.4904 target = 0.191909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.149641 restraints weight = 19358.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.153033 restraints weight = 13842.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.155357 restraints weight = 10957.181| |-----------------------------------------------------------------------------| r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9032 Z= 0.199 Angle : 0.749 12.151 12233 Z= 0.374 Chirality : 0.048 0.193 1337 Planarity : 0.005 0.049 1568 Dihedral : 6.431 29.740 1184 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % 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: -4.08 (0.23), residues: 1065 helix: -2.68 (0.41), residues: 112 sheet: -2.79 (0.37), residues: 166 loop : -2.92 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 414 HIS 0.013 0.001 HIS C 417 PHE 0.049 0.002 PHE C 475 TYR 0.023 0.002 TYR C 430 ARG 0.010 0.000 ARG A 236 *********************** 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 157 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.085 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 11 MET cc_start: 0.6164 (mpp) cc_final: 0.5584 (tpt) REVERT: A 38 MET cc_start: 0.4156 (mmm) cc_final: 0.3926 (tpt) REVERT: A 83 ARG cc_start: 0.6603 (mmm160) cc_final: 0.5885 (mmt180) REVERT: A 100 HIS cc_start: 0.6830 (m-70) cc_final: 0.6594 (m-70) REVERT: A 110 MET cc_start: 0.7728 (mmm) cc_final: 0.7310 (mmm) REVERT: A 343 ASN cc_start: 0.8297 (t0) cc_final: 0.8081 (t0) REVERT: A 360 LEU cc_start: 0.7803 (mm) cc_final: 0.7065 (tt) REVERT: A 513 GLN cc_start: 0.7352 (tp-100) cc_final: 0.6674 (mp10) REVERT: A 616 LYS cc_start: 0.8799 (tptp) cc_final: 0.8546 (tppt) REVERT: A 765 LYS cc_start: 0.7411 (mttp) cc_final: 0.6626 (mttm) REVERT: A 783 LEU cc_start: 0.8759 (tp) cc_final: 0.8429 (mt) REVERT: C 382 PHE cc_start: 0.8504 (t80) cc_final: 0.8076 (t80) REVERT: C 403 LEU cc_start: 0.6091 (tp) cc_final: 0.5519 (tt) REVERT: C 430 TYR cc_start: 0.6796 (t80) cc_final: 0.6495 (t80) REVERT: C 552 LEU cc_start: 0.9184 (tp) cc_final: 0.8081 (tp) REVERT: C 553 MET cc_start: 0.8440 (mtt) cc_final: 0.7975 (mtp) REVERT: C 780 ARG cc_start: 0.6241 (ttt-90) cc_final: 0.5291 (mtp85) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2108 time to fit residues: 45.6139 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 : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 83 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 46 optimal weight: 0.0980 chunk 31 optimal weight: 6.9990 chunk 23 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 49 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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** C 417 HIS ** C 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4925 r_free = 0.4925 target = 0.193583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.163257 restraints weight = 18971.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4618 r_free = 0.4618 target = 0.166199 restraints weight = 21055.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4626 r_free = 0.4626 target = 0.167226 restraints weight = 16727.595| |-----------------------------------------------------------------------------| r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9032 Z= 0.186 Angle : 0.723 11.976 12233 Z= 0.364 Chirality : 0.048 0.189 1337 Planarity : 0.005 0.053 1568 Dihedral : 6.202 27.409 1184 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % 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: -3.89 (0.24), residues: 1065 helix: -2.59 (0.43), residues: 113 sheet: -2.61 (0.38), residues: 166 loop : -2.79 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 412 HIS 0.011 0.001 HIS C 417 PHE 0.042 0.002 PHE C 475 TYR 0.024 0.002 TYR C 430 ARG 0.023 0.001 ARG A 65 *********************** 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 156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.951 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 11 MET cc_start: 0.6991 (mpp) cc_final: 0.5933 (tpt) REVERT: A 83 ARG cc_start: 0.6230 (mmm160) cc_final: 0.5487 (mmt180) REVERT: A 90 ASN cc_start: 0.7815 (p0) cc_final: 0.7475 (p0) REVERT: A 100 HIS cc_start: 0.6473 (m-70) cc_final: 0.6205 (m-70) REVERT: A 102 LYS cc_start: 0.7117 (pttp) cc_final: 0.6902 (pptt) REVERT: A 110 MET cc_start: 0.7673 (mmm) cc_final: 0.7341 (mmm) REVERT: A 343 ASN cc_start: 0.8241 (t0) cc_final: 0.7980 (t0) REVERT: A 360 LEU cc_start: 0.7675 (mm) cc_final: 0.6993 (tt) REVERT: A 513 GLN cc_start: 0.7311 (tp-100) cc_final: 0.6571 (mp10) REVERT: A 616 LYS cc_start: 0.8644 (tptp) cc_final: 0.8359 (tppt) REVERT: A 765 LYS cc_start: 0.7010 (mttp) cc_final: 0.6381 (mttm) REVERT: A 783 LEU cc_start: 0.8829 (tp) cc_final: 0.8431 (mt) REVERT: C 430 TYR cc_start: 0.6675 (t80) cc_final: 0.6466 (t80) REVERT: C 557 LYS cc_start: 0.6626 (mmtt) cc_final: 0.6102 (mmmt) REVERT: C 780 ARG cc_start: 0.6449 (ttt-90) cc_final: 0.5560 (mtp85) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2475 time to fit residues: 52.6418 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 : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 32 optimal weight: 8.9990 chunk 30 optimal weight: 0.2980 chunk 98 optimal weight: 0.4980 chunk 73 optimal weight: 9.9990 chunk 60 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 97 optimal weight: 0.1980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 295 ASN A 594 ASN C 417 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.189302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.146462 restraints weight = 19083.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.149641 restraints weight = 13777.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.151770 restraints weight = 11027.786| |-----------------------------------------------------------------------------| r_work (final): 0.4385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6495 moved from start: 0.4466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9032 Z= 0.225 Angle : 0.741 11.864 12233 Z= 0.374 Chirality : 0.048 0.188 1337 Planarity : 0.005 0.051 1568 Dihedral : 6.249 26.582 1184 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 0.10 % Allowed : 0.30 % Favored : 99.60 % 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: -3.99 (0.23), residues: 1065 helix: -2.67 (0.41), residues: 119 sheet: -2.85 (0.39), residues: 157 loop : -2.83 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 412 HIS 0.009 0.001 HIS C 417 PHE 0.045 0.002 PHE C 475 TYR 0.022 0.002 TYR A 144 ARG 0.007 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 151 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.978 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 11 MET cc_start: 0.6389 (mpp) cc_final: 0.5518 (tpp) REVERT: A 83 ARG cc_start: 0.6304 (mmm160) cc_final: 0.5536 (mmt180) REVERT: A 90 ASN cc_start: 0.7990 (p0) cc_final: 0.7681 (p0) REVERT: A 100 HIS cc_start: 0.6843 (m-70) cc_final: 0.6501 (m-70) REVERT: A 102 LYS cc_start: 0.7142 (pttp) cc_final: 0.6939 (pptt) REVERT: A 110 MET cc_start: 0.7775 (mmm) cc_final: 0.7369 (mmm) REVERT: A 343 ASN cc_start: 0.8315 (t0) cc_final: 0.8070 (t0) REVERT: A 360 LEU cc_start: 0.7774 (mm) cc_final: 0.7040 (tt) REVERT: A 513 GLN cc_start: 0.7270 (tp-100) cc_final: 0.6517 (mp10) REVERT: A 562 TYR cc_start: 0.7109 (m-80) cc_final: 0.6867 (m-10) REVERT: A 765 LYS cc_start: 0.7423 (mttp) cc_final: 0.6708 (mttm) REVERT: A 783 LEU cc_start: 0.8771 (tp) cc_final: 0.8456 (mt) REVERT: C 403 LEU cc_start: 0.5742 (tp) cc_final: 0.5510 (tt) REVERT: C 430 TYR cc_start: 0.6959 (t80) cc_final: 0.6624 (t80) REVERT: C 518 PHE cc_start: 0.7520 (t80) cc_final: 0.7220 (t80) REVERT: C 552 LEU cc_start: 0.9195 (tp) cc_final: 0.8990 (tp) REVERT: C 557 LYS cc_start: 0.6336 (mmtt) cc_final: 0.5772 (mmmt) REVERT: C 780 ARG cc_start: 0.6199 (ttt-90) cc_final: 0.5255 (mtp85) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.2332 time to fit residues: 47.4519 Evaluate side-chains 121 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 0.0970 chunk 37 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 101 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.0380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 417 HIS ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.193112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.162423 restraints weight = 19099.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.165438 restraints weight = 20500.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.166728 restraints weight = 17276.877| |-----------------------------------------------------------------------------| r_work (final): 0.4523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9032 Z= 0.197 Angle : 0.720 11.166 12233 Z= 0.366 Chirality : 0.048 0.189 1337 Planarity : 0.005 0.054 1568 Dihedral : 6.112 25.668 1184 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -3.86 (0.24), residues: 1065 helix: -2.66 (0.42), residues: 116 sheet: -2.84 (0.39), residues: 158 loop : -2.70 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 412 HIS 0.012 0.001 HIS C 417 PHE 0.043 0.002 PHE C 475 TYR 0.026 0.002 TYR A 374 ARG 0.007 0.000 ARG A 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3511.83 seconds wall clock time: 61 minutes 45.65 seconds (3705.65 seconds total)