Starting phenix.real_space_refine on Tue Sep 24 01:13:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/09_2024/7dqa_30816.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/09_2024/7dqa_30816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/09_2024/7dqa_30816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/09_2024/7dqa_30816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/09_2024/7dqa_30816.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dqa_30816/09_2024/7dqa_30816.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 Cl 1 4.86 5 C 4151 2.51 5 N 1070 2.21 5 O 1316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6576 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4877 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Conformer: "B" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} bond proxies already assigned to first conformer: 4998 Chain: "C" Number of atoms: 1547 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Conformer: "B" Number of residues, atoms: 194, 1541 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} bond proxies already assigned to first conformer: 1577 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 7.11, per 1000 atoms: 1.08 Number of scatterers: 6576 At special positions: 0 Unit cell: (101.362, 96.3937, 102.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Cl 1 17.00 S 37 16.00 O 1316 8.00 N 1070 7.00 C 4151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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 Links applied NAG-ASN " NAG A 903 " - " ASN A 546 " " NAG A 904 " - " ASN A 90 " " NAG A 905 " - " ASN A 322 " " NAG A 906 " - " ASN A 53 " " NAG C 601 " - " ASN C 343 " Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 378 " 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 6 sheets defined 56.9% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.847A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.749A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 88' Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 157 through 193 removed outlier: 4.612A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 300 removed outlier: 3.601A pdb=" N GLN A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.703A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.722A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.772A pdb=" N ALA A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 449 through 465 Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.725A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 503 removed outlier: 3.870A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.131A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.757A pdb=" N SER A 563 " --> pdb=" O LEU A 560 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 560 through 564' Processing helix chain 'A' and resid 565 through 575 Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'C' and resid 337 through 344 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 385 through 390 removed outlier: 4.034A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.153A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AA5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AA6, first strand: chain 'C' and resid 473 through 474 319 hydrogen bonds defined for protein. 905 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: 1.65 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2085 1.35 - 1.47: 1808 1.47 - 1.60: 2726 1.60 - 1.72: 0 1.72 - 1.85: 58 Bond restraints: 6677 Sorted by residual: bond pdb=" N CYS A 498 " pdb=" CA CYS A 498 " ideal model delta sigma weight residual 1.460 1.428 0.031 1.50e-02 4.44e+03 4.37e+00 bond pdb=" C1 NAG A 905 " pdb=" O5 NAG A 905 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.26e+00 bond pdb=" CB VAL A 581 " pdb=" CG1 VAL A 581 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.01e+00 bond pdb=" C1 NAG A 906 " pdb=" O5 NAG A 906 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.63e+00 bond pdb=" CB TRP A 566 " pdb=" CG TRP A 566 " ideal model delta sigma weight residual 1.498 1.451 0.047 3.10e-02 1.04e+03 2.27e+00 ... (remaining 6672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 8944 2.78 - 5.57: 120 5.57 - 8.35: 12 8.35 - 11.13: 2 11.13 - 13.91: 1 Bond angle restraints: 9079 Sorted by residual: angle pdb=" CA CYS A 141 " pdb=" CB CYS A 141 " pdb=" SG CYS A 141 " ideal model delta sigma weight residual 114.40 123.74 -9.34 2.30e+00 1.89e-01 1.65e+01 angle pdb=" C VAL A 581 " pdb=" CA VAL A 581 " pdb=" CB VAL A 581 " ideal model delta sigma weight residual 111.85 106.72 5.13 1.27e+00 6.20e-01 1.63e+01 angle pdb=" CA LEU A 73 " pdb=" CB LEU A 73 " pdb=" CG LEU A 73 " ideal model delta sigma weight residual 116.30 130.21 -13.91 3.50e+00 8.16e-02 1.58e+01 angle pdb=" N CYS A 498 " pdb=" CA CYS A 498 " pdb=" C CYS A 498 " ideal model delta sigma weight residual 110.06 104.49 5.57 1.43e+00 4.89e-01 1.52e+01 angle pdb=" C PHE C 497 " pdb=" N GLN C 498 " pdb=" CA GLN C 498 " ideal model delta sigma weight residual 122.48 116.77 5.71 1.62e+00 3.81e-01 1.24e+01 ... (remaining 9074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 3452 17.91 - 35.83: 402 35.83 - 53.74: 116 53.74 - 71.65: 28 71.65 - 89.56: 11 Dihedral angle restraints: 4009 sinusoidal: 1679 harmonic: 2330 Sorted by residual: dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N LEU A 142 " pdb=" CA LEU A 142 " ideal model delta harmonic sigma weight residual -180.00 -152.75 -27.25 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA LEU C 390 " pdb=" C LEU C 390 " pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta harmonic sigma weight residual -180.00 -154.18 -25.82 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA VAL C 524 " pdb=" C VAL C 524 " pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 4006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 679 0.052 - 0.104: 244 0.104 - 0.156: 38 0.156 - 0.209: 1 0.209 - 0.261: 2 Chirality restraints: 964 Sorted by residual: chirality pdb=" C1 NAG A 905 " pdb=" ND2 ASN A 322 " pdb=" C2 NAG A 905 " pdb=" O5 NAG A 905 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C1 NAG A 906 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 906 " pdb=" O5 NAG A 906 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA CYS C 432 " pdb=" N CYS C 432 " pdb=" C CYS C 432 " pdb=" CB CYS C 432 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 ... (remaining 961 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 498 " -0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO C 499 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO C 499 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 499 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 234 " 0.029 5.00e-02 4.00e+02 4.45e-02 3.16e+00 pdb=" N PRO A 235 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 235 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 235 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 498 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.82e+00 pdb=" C CYS A 498 " 0.029 2.00e-02 2.50e+03 pdb=" O CYS A 498 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP A 499 " -0.010 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 102 2.51 - 3.11: 5149 3.11 - 3.71: 10900 3.71 - 4.30: 15977 4.30 - 4.90: 25314 Nonbonded interactions: 57442 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 901 " model vdw 1.918 2.230 nonbonded pdb=" O PHE A 327 " pdb=" OG SER A 331 " model vdw 2.007 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.043 3.040 nonbonded pdb=" O HOH A1022 " pdb=" O HOH A1034 " model vdw 2.069 3.040 nonbonded pdb=" O HOH A1011 " pdb=" O HOH A1052 " model vdw 2.100 3.040 ... (remaining 57437 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.690 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.350 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: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 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 : 0.007 0.066 6677 Z= 0.485 Angle : 0.863 13.914 9079 Z= 0.492 Chirality : 0.051 0.261 964 Planarity : 0.005 0.065 1173 Dihedral : 17.506 89.563 2494 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 18.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 6.03 % Allowed : 19.80 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -3.29 (0.24), residues: 789 helix: -2.34 (0.19), residues: 393 sheet: -1.53 (0.62), residues: 58 loop : -1.91 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 48 HIS 0.006 0.002 HIS A 34 PHE 0.016 0.003 PHE A 285 TYR 0.021 0.002 TYR C 495 ARG 0.008 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 147 time to evaluate : 0.632 Fit side-chains REVERT: A 23 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6902 (mm-30) REVERT: A 30 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6469 (t0) REVERT: A 62 MET cc_start: 0.7554 (ttt) cc_final: 0.7204 (ttp) REVERT: A 68 LYS cc_start: 0.6424 (mtpp) cc_final: 0.6189 (tttm) REVERT: A 73 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.4740 (mt) REVERT: A 131 LYS cc_start: 0.7440 (ptpp) cc_final: 0.7196 (ptmm) REVERT: A 136 ASP cc_start: 0.3336 (OUTLIER) cc_final: 0.2870 (p0) REVERT: A 146 PRO cc_start: 0.6097 (Cg_endo) cc_final: 0.5814 (Cg_exo) REVERT: A 151 ILE cc_start: 0.6579 (mt) cc_final: 0.5640 (mp) REVERT: A 159 ASN cc_start: 0.6007 (m-40) cc_final: 0.5716 (m110) REVERT: A 249 MET cc_start: 0.5732 (ptt) cc_final: 0.5487 (ttp) REVERT: A 313 LYS cc_start: 0.6775 (ttmt) cc_final: 0.6532 (mtpp) REVERT: A 314 PHE cc_start: 0.7063 (t80) cc_final: 0.6496 (t80) REVERT: A 341 LYS cc_start: 0.6040 (tptt) cc_final: 0.5729 (tttm) REVERT: A 368 ASP cc_start: 0.7211 (t0) cc_final: 0.6560 (m-30) REVERT: A 401 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8186 (m-70) REVERT: A 429 GLN cc_start: 0.5970 (OUTLIER) cc_final: 0.5184 (tm-30) REVERT: A 540 HIS cc_start: 0.7053 (p-80) cc_final: 0.6777 (p90) REVERT: A 600 LYS cc_start: 0.6515 (mtmt) cc_final: 0.6286 (mtmm) REVERT: C 356 LYS cc_start: 0.6965 (mptt) cc_final: 0.6707 (mtpp) REVERT: C 459 SER cc_start: 0.6597 (OUTLIER) cc_final: 0.6086 (p) REVERT: C 467 ASP cc_start: 0.5688 (t0) cc_final: 0.5427 (t0) REVERT: C 516 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4887 (pp20) outliers start: 40 outliers final: 6 residues processed: 183 average time/residue: 0.9861 time to fit residues: 190.9421 Evaluate side-chains 106 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 93 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 429 GLN Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 516 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 117 ASN A 194 ASN A 239 HIS A 325 GLN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 531 GLN A 535 HIS A 580 ASN C 388 ASN C 450 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6677 Z= 0.223 Angle : 0.658 8.391 9079 Z= 0.345 Chirality : 0.044 0.180 964 Planarity : 0.005 0.039 1173 Dihedral : 7.825 61.860 989 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.30 % Allowed : 25.11 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -1.06 (0.27), residues: 789 helix: -0.39 (0.23), residues: 399 sheet: -1.35 (0.69), residues: 47 loop : -0.82 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.011 0.001 HIS A 374 PHE 0.018 0.002 PHE A 588 TYR 0.016 0.002 TYR A 385 ARG 0.008 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.654 Fit side-chains REVERT: A 23 GLU cc_start: 0.7260 (mm-30) cc_final: 0.6987 (mm-30) REVERT: A 131 LYS cc_start: 0.7693 (ptpp) cc_final: 0.7418 (ptmm) REVERT: A 151 ILE cc_start: 0.6124 (mt) cc_final: 0.5753 (mp) REVERT: A 179 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8080 (mt) REVERT: A 341 LYS cc_start: 0.5891 (tptt) cc_final: 0.5499 (tttm) REVERT: A 383 MET cc_start: 0.7618 (mtp) cc_final: 0.7297 (mtm) REVERT: A 408 MET cc_start: 0.7735 (OUTLIER) cc_final: 0.7015 (mmt) REVERT: A 476 LYS cc_start: 0.7576 (tppt) cc_final: 0.7315 (tppp) REVERT: A 597 ASP cc_start: 0.6052 (t0) cc_final: 0.5834 (t70) REVERT: C 356 LYS cc_start: 0.7164 (mptt) cc_final: 0.6719 (mtpp) REVERT: C 418 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.7247 (mm) REVERT: C 467 ASP cc_start: 0.5611 (t0) cc_final: 0.5335 (t0) outliers start: 21 outliers final: 4 residues processed: 124 average time/residue: 1.0717 time to fit residues: 140.7784 Evaluate side-chains 96 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain C residue 418 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.0050 chunk 70 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6677 Z= 0.216 Angle : 0.617 10.213 9079 Z= 0.322 Chirality : 0.044 0.196 964 Planarity : 0.004 0.037 1173 Dihedral : 5.498 36.821 968 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.01 % Allowed : 25.68 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.29), residues: 789 helix: 0.31 (0.25), residues: 400 sheet: -0.92 (0.67), residues: 46 loop : -0.41 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.008 0.001 HIS A 195 PHE 0.029 0.002 PHE A 285 TYR 0.017 0.002 TYR A 521 ARG 0.006 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.728 Fit side-chains REVERT: A 61 ASN cc_start: 0.6970 (t0) cc_final: 0.6614 (m-40) REVERT: A 131 LYS cc_start: 0.7810 (ptpp) cc_final: 0.7340 (ptmm) REVERT: A 151 ILE cc_start: 0.6209 (mt) cc_final: 0.5834 (mp) REVERT: A 171 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6420 (mp0) REVERT: A 179 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8086 (mt) REVERT: A 194 ASN cc_start: 0.7465 (OUTLIER) cc_final: 0.7151 (t0) REVERT: A 341 LYS cc_start: 0.6018 (tptt) cc_final: 0.5575 (tttm) REVERT: A 383 MET cc_start: 0.7600 (mtp) cc_final: 0.7330 (mtm) REVERT: A 408 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7040 (mmt) REVERT: A 476 LYS cc_start: 0.7520 (tppt) cc_final: 0.7287 (tppp) REVERT: C 356 LYS cc_start: 0.7123 (mptt) cc_final: 0.6799 (tttp) REVERT: C 467 ASP cc_start: 0.5612 (t0) cc_final: 0.5272 (t0) REVERT: C 468 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6647 (mm) outliers start: 19 outliers final: 5 residues processed: 105 average time/residue: 1.0377 time to fit residues: 115.8497 Evaluate side-chains 93 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS C 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6677 Z= 0.185 Angle : 0.588 11.378 9079 Z= 0.305 Chirality : 0.043 0.185 964 Planarity : 0.004 0.036 1173 Dihedral : 5.023 35.873 968 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.59 % Allowed : 24.68 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.29), residues: 789 helix: 0.71 (0.25), residues: 399 sheet: -0.79 (0.69), residues: 46 loop : -0.27 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.010 0.001 HIS A 195 PHE 0.012 0.001 PHE A 315 TYR 0.019 0.002 TYR A 521 ARG 0.004 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 61 ASN cc_start: 0.7011 (t0) cc_final: 0.6681 (m-40) REVERT: A 114 LYS cc_start: 0.7156 (ptmm) cc_final: 0.6356 (pttp) REVERT: A 121 ASN cc_start: 0.7128 (m-40) cc_final: 0.6318 (t0) REVERT: A 128 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7559 (p) REVERT: A 131 LYS cc_start: 0.7790 (ptpp) cc_final: 0.7381 (ptmm) REVERT: A 143 LEU cc_start: 0.7928 (mt) cc_final: 0.7727 (mt) REVERT: A 145 GLU cc_start: 0.6739 (tp30) cc_final: 0.6493 (tp30) REVERT: A 146 PRO cc_start: 0.6823 (Cg_endo) cc_final: 0.6002 (Cg_exo) REVERT: A 171 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.5890 (mp0) REVERT: A 179 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8096 (mt) REVERT: A 249 MET cc_start: 0.5418 (mtp) cc_final: 0.5075 (ttp) REVERT: A 297 MET cc_start: 0.6636 (mtm) cc_final: 0.5922 (mtp) REVERT: A 341 LYS cc_start: 0.6040 (tptt) cc_final: 0.5561 (tttm) REVERT: A 383 MET cc_start: 0.7506 (mtp) cc_final: 0.7216 (mtm) REVERT: C 356 LYS cc_start: 0.7147 (mptt) cc_final: 0.6850 (tttp) REVERT: C 446 GLU cc_start: 0.5162 (OUTLIER) cc_final: 0.4615 (mm-30) REVERT: C 467 ASP cc_start: 0.5686 (t0) cc_final: 0.5265 (t0) REVERT: C 468 ILE cc_start: 0.6882 (OUTLIER) cc_final: 0.6612 (mm) outliers start: 23 outliers final: 7 residues processed: 111 average time/residue: 1.0212 time to fit residues: 120.4673 Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 446 GLU Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6677 Z= 0.198 Angle : 0.593 10.393 9079 Z= 0.307 Chirality : 0.043 0.180 964 Planarity : 0.004 0.033 1173 Dihedral : 4.930 35.932 968 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.16 % Allowed : 25.25 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.29), residues: 789 helix: 0.85 (0.26), residues: 400 sheet: -0.43 (0.74), residues: 47 loop : -0.20 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.014 0.002 PHE A 285 TYR 0.021 0.002 TYR A 521 ARG 0.004 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.704 Fit side-chains REVERT: A 61 ASN cc_start: 0.7028 (t0) cc_final: 0.6727 (m-40) REVERT: A 114 LYS cc_start: 0.7093 (ptmm) cc_final: 0.6331 (pttp) REVERT: A 121 ASN cc_start: 0.7136 (m-40) cc_final: 0.6344 (t0) REVERT: A 128 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.7547 (p) REVERT: A 131 LYS cc_start: 0.7826 (ptpp) cc_final: 0.7341 (ptmm) REVERT: A 143 LEU cc_start: 0.7809 (mt) cc_final: 0.7541 (mt) REVERT: A 146 PRO cc_start: 0.6855 (Cg_endo) cc_final: 0.6424 (Cg_exo) REVERT: A 171 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.5749 (mp0) REVERT: A 179 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8118 (mt) REVERT: A 249 MET cc_start: 0.5441 (mtp) cc_final: 0.5128 (ttp) REVERT: A 297 MET cc_start: 0.6745 (mtm) cc_final: 0.6031 (mtt) REVERT: A 341 LYS cc_start: 0.6123 (tptt) cc_final: 0.5642 (tttm) REVERT: A 383 MET cc_start: 0.7559 (mtp) cc_final: 0.7296 (mtm) REVERT: A 470 LYS cc_start: 0.7780 (mtpt) cc_final: 0.6875 (tptt) REVERT: A 476 LYS cc_start: 0.7506 (tppt) cc_final: 0.7270 (tppp) REVERT: C 356 LYS cc_start: 0.7355 (mptt) cc_final: 0.7027 (tttp) REVERT: C 467 ASP cc_start: 0.5758 (t0) cc_final: 0.5365 (t0) REVERT: C 468 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6584 (mm) outliers start: 20 outliers final: 9 residues processed: 100 average time/residue: 1.0127 time to fit residues: 107.7386 Evaluate side-chains 90 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 77 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 0.0270 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 72 optimal weight: 0.3980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS C 474 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6677 Z= 0.174 Angle : 0.562 8.425 9079 Z= 0.291 Chirality : 0.042 0.141 964 Planarity : 0.004 0.033 1173 Dihedral : 4.739 35.941 968 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.16 % Allowed : 25.25 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.29), residues: 789 helix: 0.90 (0.26), residues: 409 sheet: -0.29 (0.79), residues: 45 loop : -0.29 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 594 HIS 0.004 0.001 HIS A 540 PHE 0.010 0.001 PHE A 315 TYR 0.015 0.001 TYR A 385 ARG 0.003 0.001 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.639 Fit side-chains REVERT: A 61 ASN cc_start: 0.6992 (t0) cc_final: 0.6750 (m-40) REVERT: A 114 LYS cc_start: 0.7171 (ptmm) cc_final: 0.6276 (pttp) REVERT: A 121 ASN cc_start: 0.7155 (m-40) cc_final: 0.6372 (t0) REVERT: A 128 SER cc_start: 0.7839 (OUTLIER) cc_final: 0.7513 (p) REVERT: A 131 LYS cc_start: 0.7961 (ptpp) cc_final: 0.7469 (ptmm) REVERT: A 143 LEU cc_start: 0.7798 (mt) cc_final: 0.7404 (mt) REVERT: A 146 PRO cc_start: 0.6902 (Cg_endo) cc_final: 0.6469 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6497 (m-40) cc_final: 0.6035 (t0) REVERT: A 163 TRP cc_start: 0.6920 (t60) cc_final: 0.6704 (t60) REVERT: A 171 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.5737 (mp0) REVERT: A 179 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8131 (mt) REVERT: A 249 MET cc_start: 0.5552 (mtp) cc_final: 0.5101 (ttp) REVERT: A 341 LYS cc_start: 0.6117 (tptt) cc_final: 0.5624 (tttm) REVERT: A 383 MET cc_start: 0.7460 (mtp) cc_final: 0.7232 (mtm) REVERT: C 356 LYS cc_start: 0.7240 (mptt) cc_final: 0.6906 (tttp) REVERT: C 406 GLU cc_start: 0.7952 (mp0) cc_final: 0.7417 (mt-10) REVERT: C 467 ASP cc_start: 0.5822 (t0) cc_final: 0.5392 (t0) REVERT: C 468 ILE cc_start: 0.6817 (OUTLIER) cc_final: 0.6431 (mm) outliers start: 20 outliers final: 8 residues processed: 100 average time/residue: 1.0055 time to fit residues: 106.8217 Evaluate side-chains 96 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0270 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 0.0060 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 overall best weight: 0.8056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6729 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6677 Z= 0.186 Angle : 0.572 7.603 9079 Z= 0.294 Chirality : 0.042 0.136 964 Planarity : 0.004 0.032 1173 Dihedral : 4.701 36.275 968 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.73 % Allowed : 26.11 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.30), residues: 789 helix: 0.95 (0.26), residues: 409 sheet: -0.10 (0.83), residues: 45 loop : -0.27 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.012 0.001 PHE A 285 TYR 0.022 0.001 TYR A 521 ARG 0.003 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.767 Fit side-chains REVERT: A 61 ASN cc_start: 0.6975 (t0) cc_final: 0.6774 (m-40) REVERT: A 114 LYS cc_start: 0.7247 (ptmm) cc_final: 0.6359 (pttp) REVERT: A 121 ASN cc_start: 0.7155 (m-40) cc_final: 0.6416 (t0) REVERT: A 128 SER cc_start: 0.7820 (OUTLIER) cc_final: 0.7484 (p) REVERT: A 131 LYS cc_start: 0.7969 (ptpp) cc_final: 0.7443 (ptmm) REVERT: A 143 LEU cc_start: 0.7846 (mt) cc_final: 0.7507 (mt) REVERT: A 146 PRO cc_start: 0.6924 (Cg_endo) cc_final: 0.6509 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6675 (m-40) cc_final: 0.6114 (t0) REVERT: A 171 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.5772 (mp0) REVERT: A 179 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 249 MET cc_start: 0.5592 (mtp) cc_final: 0.5115 (ttp) REVERT: A 341 LYS cc_start: 0.6063 (tptt) cc_final: 0.5608 (tttm) REVERT: A 383 MET cc_start: 0.7555 (mtp) cc_final: 0.7303 (mtm) REVERT: A 470 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7044 (tptt) REVERT: A 474 MET cc_start: 0.7650 (mmp) cc_final: 0.7091 (mmp) REVERT: C 467 ASP cc_start: 0.5850 (t0) cc_final: 0.5420 (t0) REVERT: C 468 ILE cc_start: 0.6835 (OUTLIER) cc_final: 0.6455 (mm) outliers start: 17 outliers final: 10 residues processed: 100 average time/residue: 1.0531 time to fit residues: 111.5724 Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS C 474 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6677 Z= 0.206 Angle : 0.589 7.723 9079 Z= 0.303 Chirality : 0.043 0.138 964 Planarity : 0.004 0.032 1173 Dihedral : 4.726 34.911 968 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.58 % Allowed : 26.26 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.30), residues: 789 helix: 0.98 (0.26), residues: 403 sheet: -0.07 (0.83), residues: 45 loop : -0.24 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.011 0.002 PHE A 523 TYR 0.016 0.001 TYR A 385 ARG 0.005 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 83 time to evaluate : 0.719 Fit side-chains REVERT: A 61 ASN cc_start: 0.6989 (t0) cc_final: 0.6775 (m-40) REVERT: A 114 LYS cc_start: 0.7265 (ptmm) cc_final: 0.6354 (pttp) REVERT: A 121 ASN cc_start: 0.7153 (m-40) cc_final: 0.6361 (t0) REVERT: A 128 SER cc_start: 0.7799 (OUTLIER) cc_final: 0.7468 (p) REVERT: A 131 LYS cc_start: 0.7921 (ptpp) cc_final: 0.7269 (ptmm) REVERT: A 143 LEU cc_start: 0.7795 (mt) cc_final: 0.7469 (mt) REVERT: A 146 PRO cc_start: 0.7184 (Cg_endo) cc_final: 0.6738 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6729 (m-40) cc_final: 0.6173 (t0) REVERT: A 171 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.5810 (mp0) REVERT: A 179 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8083 (mt) REVERT: A 249 MET cc_start: 0.5567 (mtp) cc_final: 0.5138 (ttp) REVERT: A 341 LYS cc_start: 0.6243 (tptt) cc_final: 0.5754 (tttm) REVERT: A 383 MET cc_start: 0.7632 (mtp) cc_final: 0.7324 (mtm) REVERT: A 474 MET cc_start: 0.7666 (mmp) cc_final: 0.7223 (mmp) REVERT: A 531 GLN cc_start: 0.7210 (mt0) cc_final: 0.6780 (mp10) REVERT: C 467 ASP cc_start: 0.5883 (t0) cc_final: 0.5457 (t0) outliers start: 16 outliers final: 9 residues processed: 95 average time/residue: 1.1692 time to fit residues: 117.3878 Evaluate side-chains 91 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain C residue 443 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS C 474 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6677 Z= 0.233 Angle : 0.613 7.849 9079 Z= 0.315 Chirality : 0.043 0.137 964 Planarity : 0.004 0.031 1173 Dihedral : 4.822 34.850 968 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.44 % Allowed : 26.26 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.30), residues: 789 helix: 0.90 (0.26), residues: 403 sheet: -0.02 (0.84), residues: 45 loop : -0.25 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.018 0.002 PHE A 588 TYR 0.023 0.002 TYR A 521 ARG 0.005 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.669 Fit side-chains REVERT: A 37 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6115 (tp30) REVERT: A 61 ASN cc_start: 0.7021 (t0) cc_final: 0.6783 (m-40) REVERT: A 114 LYS cc_start: 0.7301 (ptmm) cc_final: 0.6378 (pttp) REVERT: A 128 SER cc_start: 0.7804 (OUTLIER) cc_final: 0.7449 (p) REVERT: A 131 LYS cc_start: 0.8009 (ptpp) cc_final: 0.7501 (ptmm) REVERT: A 143 LEU cc_start: 0.7709 (mt) cc_final: 0.7399 (mt) REVERT: A 146 PRO cc_start: 0.7252 (Cg_endo) cc_final: 0.6845 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6905 (m-40) cc_final: 0.6366 (t0) REVERT: A 171 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.5874 (mp0) REVERT: A 179 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8068 (mt) REVERT: A 249 MET cc_start: 0.5665 (mtp) cc_final: 0.5175 (ttp) REVERT: A 341 LYS cc_start: 0.6218 (tptt) cc_final: 0.5769 (tttm) REVERT: A 383 MET cc_start: 0.7636 (mtp) cc_final: 0.7294 (mtm) REVERT: A 474 MET cc_start: 0.7678 (mmp) cc_final: 0.7195 (mmp) REVERT: A 531 GLN cc_start: 0.7208 (mt0) cc_final: 0.6796 (mp10) REVERT: C 351 TYR cc_start: 0.7229 (p90) cc_final: 0.6767 (p90) REVERT: C 467 ASP cc_start: 0.6034 (t0) cc_final: 0.5679 (t0) REVERT: C 468 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6424 (mm) outliers start: 15 outliers final: 8 residues processed: 94 average time/residue: 1.1961 time to fit residues: 118.6864 Evaluate side-chains 93 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS C 474 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6677 Z= 0.189 Angle : 0.583 7.945 9079 Z= 0.300 Chirality : 0.042 0.136 964 Planarity : 0.004 0.032 1173 Dihedral : 4.659 34.455 968 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.30 % Allowed : 26.26 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.30), residues: 789 helix: 0.97 (0.26), residues: 408 sheet: -0.03 (0.83), residues: 45 loop : -0.23 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.016 0.001 PHE C 486 TYR 0.024 0.001 TYR A 521 ARG 0.005 0.001 ARG A 482 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1578 Ramachandran restraints generated. 789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.729 Fit side-chains REVERT: A 37 GLU cc_start: 0.6471 (OUTLIER) cc_final: 0.6056 (tp30) REVERT: A 114 LYS cc_start: 0.7305 (ptmm) cc_final: 0.6382 (pttp) REVERT: A 121 ASN cc_start: 0.7314 (m-40) cc_final: 0.6509 (t0) REVERT: A 128 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7482 (p) REVERT: A 131 LYS cc_start: 0.7952 (ptpp) cc_final: 0.7243 (ptmm) REVERT: A 143 LEU cc_start: 0.7717 (mt) cc_final: 0.7439 (mt) REVERT: A 146 PRO cc_start: 0.7226 (Cg_endo) cc_final: 0.6840 (Cg_exo) REVERT: A 159 ASN cc_start: 0.6889 (m-40) cc_final: 0.6340 (t0) REVERT: A 171 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.5778 (mp0) REVERT: A 179 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8065 (mt) REVERT: A 249 MET cc_start: 0.5539 (mtp) cc_final: 0.5143 (OUTLIER) REVERT: A 341 LYS cc_start: 0.6232 (tptt) cc_final: 0.5766 (tttm) REVERT: A 383 MET cc_start: 0.7540 (mtp) cc_final: 0.7287 (mtm) REVERT: A 474 MET cc_start: 0.7566 (mmp) cc_final: 0.7241 (mmp) REVERT: A 531 GLN cc_start: 0.7200 (mt0) cc_final: 0.6799 (mp10) REVERT: C 467 ASP cc_start: 0.6023 (t0) cc_final: 0.5637 (t0) REVERT: C 468 ILE cc_start: 0.6752 (OUTLIER) cc_final: 0.6394 (mm) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 1.1333 time to fit residues: 113.8845 Evaluate side-chains 92 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 37 GLU Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 128 SER Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain C residue 443 SER Chi-restraints excluded: chain C residue 468 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 7 optimal weight: 0.0470 chunk 11 optimal weight: 10.0000 chunk 54 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 ASN ** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.182823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.152267 restraints weight = 11097.591| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 1.88 r_work: 0.3618 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6677 Z= 0.170 Angle : 0.564 8.008 9079 Z= 0.291 Chirality : 0.042 0.136 964 Planarity : 0.004 0.033 1173 Dihedral : 4.490 33.540 968 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.58 % Allowed : 27.40 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.30), residues: 789 helix: 1.11 (0.26), residues: 404 sheet: -0.06 (0.83), residues: 45 loop : -0.14 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 594 HIS 0.005 0.001 HIS A 540 PHE 0.012 0.001 PHE A 588 TYR 0.027 0.001 TYR C 351 ARG 0.004 0.000 ARG A 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2833.61 seconds wall clock time: 50 minutes 13.48 seconds (3013.48 seconds total)