Starting phenix.real_space_refine on Tue Mar 11 14:30:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pg0_17655/03_2025/8pg0_17655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pg0_17655/03_2025/8pg0_17655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pg0_17655/03_2025/8pg0_17655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pg0_17655/03_2025/8pg0_17655.map" model { file = "/net/cci-nas-00/data/ceres_data/8pg0_17655/03_2025/8pg0_17655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pg0_17655/03_2025/8pg0_17655.cif" } resolution = 2.97 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= 0.001 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 38 5.16 5 C 3826 2.51 5 N 912 2.21 5 O 1040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3986 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 511, 3978 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 17, 'TRANS': 493} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 511, 3978 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 17, 'TRANS': 493} Chain breaks: 8 bond proxies already assigned to first conformer: 4066 Chain: "H" Number of atoms: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 970 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 1, 'TRANS': 123} Chain breaks: 1 Chain: "L" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 758 Classifications: {'peptide': 101} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 94} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Unusual residues: {'BCT': 1, 'CLR': 3, 'NAG': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP A 70 " occ=0.58 ... (14 atoms not shown) pdb=" OD2BASP A 70 " occ=0.42 Time building chain proxies: 7.19, per 1000 atoms: 1.24 Number of scatterers: 5816 At special positions: 0 Unit cell: (78.03, 119.85, 104.04, 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 38 16.00 O 1040 8.00 N 912 7.00 C 3826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 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 801 " - " ASN A 503 " Time building additional restraints: 1.71 Conformation dependent library (CDL) restraints added in 1.4 seconds 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1338 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 53.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 Processing helix chain 'A' and resid 51 through 60 Processing helix chain 'A' and resid 62 through 85 removed outlier: 4.048A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLU A 74 " --> pdb=" O AASP A 70 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'A' and resid 113 through 118 Processing helix chain 'A' and resid 170 through 186 removed outlier: 4.033A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 217 through 231 removed outlier: 3.966A pdb=" N VAL A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 removed outlier: 3.696A pdb=" N GLY A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) 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 325 through 335 Processing helix chain 'A' and resid 335 through 358 removed outlier: 3.928A pdb=" N TYR A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 370 through 401 Proline residue: A 384 - end of helix removed outlier: 3.946A pdb=" N PHE A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 425 Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.834A pdb=" N GLU A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 504 through 508 removed outlier: 3.888A pdb=" N GLU A 508 " --> pdb=" O SER A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 561 removed outlier: 3.940A pdb=" N THR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU A 557 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS A 561 " --> pdb=" O LEU A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 567 through 585 Processing helix chain 'A' and resid 586 through 598 removed outlier: 3.613A pdb=" N LEU A 594 " --> pdb=" O TYR A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 649 removed outlier: 4.060A pdb=" N SER A 629 " --> pdb=" O TYR A 625 " (cutoff:3.500A) Proline residue: A 635 - end of helix removed outlier: 4.008A pdb=" N LYS A 649 " --> pdb=" O PHE A 645 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.911A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.527A pdb=" N CYS A 474 " --> pdb=" O HIS A 520 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 492 removed outlier: 3.641A pdb=" N SER A 491 " --> pdb=" O TYR A 502 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 599 through 602 removed outlier: 7.000A pdb=" N CYS A 599 " --> pdb=" O TYR A 616 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR A 616 " --> pdb=" O CYS A 599 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LYS A 601 " --> pdb=" O ARG A 614 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA5, first strand: chain 'H' and resid 61 through 63 removed outlier: 6.597A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 103 through 105 removed outlier: 4.202A pdb=" N TYR H 103 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7 removed outlier: 6.793A pdb=" N GLN L 4 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR L 6 " --> pdb=" O ARG L 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 46 through 47 327 hydrogen bonds defined for protein. 946 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: 1.85 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.56: 5900 1.56 - 1.91: 59 1.91 - 2.25: 0 2.25 - 2.60: 0 2.60 - 2.95: 1 Bond restraints: 5960 Sorted by residual: bond pdb=" C TYR L 50 " pdb=" N SER L 53 " ideal model delta sigma weight residual 1.329 2.947 -1.618 1.40e-02 5.10e+03 1.34e+04 bond pdb=" C ARG A 526 " pdb=" N ASP A 527 " ideal model delta sigma weight residual 1.328 1.432 -0.104 1.44e-02 4.82e+03 5.20e+01 bond pdb=" C VAL A 221 " pdb=" N ILE A 222 " ideal model delta sigma weight residual 1.335 1.282 0.053 1.26e-02 6.30e+03 1.77e+01 bond pdb=" N VAL A 563 " pdb=" CA VAL A 563 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N GLY A 475 " pdb=" CA GLY A 475 " ideal model delta sigma weight residual 1.444 1.476 -0.031 1.06e-02 8.90e+03 8.83e+00 ... (remaining 5955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.46: 8074 7.46 - 14.92: 3 14.92 - 22.38: 0 22.38 - 29.84: 0 29.84 - 37.30: 1 Bond angle restraints: 8078 Sorted by residual: angle pdb=" C TYR L 50 " pdb=" N SER L 53 " pdb=" CA SER L 53 " ideal model delta sigma weight residual 121.70 159.00 -37.30 1.80e+00 3.09e-01 4.30e+02 angle pdb=" N ILE A 562 " pdb=" CA ILE A 562 " pdb=" C ILE A 562 " ideal model delta sigma weight residual 112.29 107.96 4.33 9.40e-01 1.13e+00 2.12e+01 angle pdb=" C SER L 10 " pdb=" CA SER L 10 " pdb=" CB SER L 10 " ideal model delta sigma weight residual 117.23 111.69 5.54 1.36e+00 5.41e-01 1.66e+01 angle pdb=" N ASN A 477 " pdb=" CA ASN A 477 " pdb=" C ASN A 477 " ideal model delta sigma weight residual 113.19 108.58 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N ASN A 476 " pdb=" CA ASN A 476 " pdb=" C ASN A 476 " ideal model delta sigma weight residual 112.87 108.30 4.57 1.20e+00 6.94e-01 1.45e+01 ... (remaining 8073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 3323 24.23 - 48.45: 246 48.45 - 72.68: 36 72.68 - 96.90: 5 96.90 - 121.13: 3 Dihedral angle restraints: 3613 sinusoidal: 1511 harmonic: 2102 Sorted by residual: dihedral pdb=" CA TYR L 50 " pdb=" C TYR L 50 " pdb=" N SER L 53 " pdb=" CA SER L 53 " ideal model delta harmonic sigma weight residual 0.00 -38.47 38.47 0 5.00e+00 4.00e-02 5.92e+01 dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 506 " pdb=" CB CYS A 506 " ideal model delta sinusoidal sigma weight residual 93.00 131.42 -38.42 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 524 " pdb=" CB CYS A 524 " ideal model delta sinusoidal sigma weight residual 93.00 55.20 37.80 1 1.00e+01 1.00e-02 2.01e+01 ... (remaining 3610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 795 0.083 - 0.166: 109 0.166 - 0.250: 19 0.250 - 0.333: 1 0.333 - 0.416: 1 Chirality restraints: 925 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 503 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C13 CLR A 805 " pdb=" C12 CLR A 805 " pdb=" C14 CLR A 805 " pdb=" C17 CLR A 805 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C14 CLR A 805 " pdb=" C13 CLR A 805 " pdb=" C15 CLR A 805 " pdb=" C8 CLR A 805 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 922 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 801 " 0.270 2.00e-02 2.50e+03 2.28e-01 6.47e+02 pdb=" C7 NAG A 801 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A 801 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG A 801 " -0.387 2.00e-02 2.50e+03 pdb=" O7 NAG A 801 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 50 " 0.023 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C TYR L 50 " -0.069 2.00e-02 2.50e+03 pdb=" O TYR L 50 " 0.032 2.00e-02 2.50e+03 pdb=" N SER L 53 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 471 " 0.053 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A 472 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 472 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 472 " 0.043 5.00e-02 4.00e+02 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 586 2.75 - 3.29: 6007 3.29 - 3.82: 9912 3.82 - 4.36: 12040 4.36 - 4.90: 20237 Nonbonded interactions: 48782 Sorted by model distance: nonbonded pdb=" OE1 GLN A 366 " pdb=" OG SER A 618 " model vdw 2.211 3.040 nonbonded pdb=" O PRO A 472 " pdb=" O LEU A 521 " model vdw 2.252 3.040 nonbonded pdb=" O SER H 33 " pdb=" OG SER H 57 " model vdw 2.280 3.040 nonbonded pdb=" O SER A 228 " pdb=" OG SER A 372 " model vdw 2.281 3.040 nonbonded pdb=" ND1 HIS A 115 " pdb=" O2 BCT A 802 " model vdw 2.299 3.120 ... (remaining 48777 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=0.42 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: 4.380 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 22.040 Find NCS groups from input model: 0.080 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:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 : 0.022 1.618 5960 Z= 1.375 Angle : 0.943 37.304 8078 Z= 0.587 Chirality : 0.058 0.416 925 Planarity : 0.009 0.228 969 Dihedral : 16.430 121.126 2251 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.22 % Favored : 95.64 % Rotamer: Outliers : 0.80 % Allowed : 24.12 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.32), residues: 714 helix: 1.26 (0.28), residues: 348 sheet: -0.12 (0.54), residues: 105 loop : -0.98 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS A 451 PHE 0.011 0.001 PHE A 175 TYR 0.018 0.001 TYR A 590 ARG 0.003 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1428 Ramachandran restraints generated. 714 Oldfield, 0 Emsley, 714 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 103 time to evaluate : 0.640 Fit side-chains REVERT: A 640 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.6864 (t80) REVERT: H 21 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.7055 (tp) outliers start: 5 outliers final: 1 residues processed: 107 average time/residue: 0.7939 time to fit residues: 90.8674 Evaluate side-chains 91 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 88 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN A 476 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 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 = 0.3975 r_free = 0.3975 target = 0.165426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139267 restraints weight = 21533.240| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.87 r_work: 0.3542 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5960 Z= 0.202 Angle : 0.644 9.282 8078 Z= 0.317 Chirality : 0.044 0.221 925 Planarity : 0.004 0.047 969 Dihedral : 7.731 78.699 1009 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 4.79 % Allowed : 22.04 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.74 (0.32), residues: 716 helix: 1.68 (0.27), residues: 352 sheet: 0.05 (0.53), residues: 108 loop : -0.97 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.002 0.001 HIS A 169 PHE 0.011 0.001 PHE A 175 TYR 0.021 0.001 TYR A 590 ARG 0.004 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.592 Fit side-chains REVERT: A 83 PHE cc_start: 0.6520 (m-10) cc_final: 0.6310 (m-80) REVERT: A 390 MET cc_start: 0.6307 (OUTLIER) cc_final: 0.5888 (ptm) REVERT: A 446 ASN cc_start: 0.6141 (m-40) cc_final: 0.5935 (m-40) REVERT: A 640 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7351 (t80) REVERT: H 21 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7279 (tp) REVERT: L 67 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5897 (ppt170) outliers start: 30 outliers final: 11 residues processed: 116 average time/residue: 0.6692 time to fit residues: 84.1649 Evaluate side-chains 103 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 390 MET Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.158357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.132363 restraints weight = 20446.241| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.74 r_work: 0.3439 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3426 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3426 r_free = 0.3426 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3426 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 5960 Z= 0.325 Angle : 0.730 12.106 8078 Z= 0.359 Chirality : 0.047 0.234 925 Planarity : 0.005 0.046 969 Dihedral : 7.860 81.398 1007 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.39 % Allowed : 21.57 % Favored : 72.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.47 (0.32), residues: 716 helix: 1.24 (0.27), residues: 354 sheet: 0.57 (0.55), residues: 92 loop : -1.00 (0.38), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 254 HIS 0.003 0.001 HIS A 92 PHE 0.017 0.002 PHE A 73 TYR 0.016 0.002 TYR A 590 ARG 0.004 0.001 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 95 time to evaluate : 0.596 Fit side-chains REVERT: A 640 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7210 (t80) REVERT: H 21 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7127 (tp) REVERT: L 48 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7227 (mt) REVERT: L 67 ARG cc_start: 0.6445 (OUTLIER) cc_final: 0.6063 (ppt170) outliers start: 40 outliers final: 19 residues processed: 115 average time/residue: 0.6819 time to fit residues: 84.5895 Evaluate side-chains 113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 474 CYS Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 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 = 0.3955 r_free = 0.3955 target = 0.163467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.137400 restraints weight = 23940.446| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.16 r_work: 0.3532 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5960 Z= 0.179 Angle : 0.621 9.081 8078 Z= 0.304 Chirality : 0.043 0.219 925 Planarity : 0.004 0.045 969 Dihedral : 7.281 76.004 1007 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.11 % Allowed : 23.16 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.69 (0.32), residues: 716 helix: 1.60 (0.27), residues: 346 sheet: 0.25 (0.53), residues: 102 loop : -0.96 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 PHE 0.011 0.001 PHE A 175 TYR 0.021 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 104 time to evaluate : 0.569 Fit side-chains REVERT: A 596 ASP cc_start: 0.7653 (m-30) cc_final: 0.7419 (m-30) REVERT: A 640 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7338 (t80) REVERT: H 21 LEU cc_start: 0.7343 (OUTLIER) cc_final: 0.7029 (tp) REVERT: L 48 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7159 (mt) REVERT: L 67 ARG cc_start: 0.6411 (OUTLIER) cc_final: 0.5870 (ppt170) outliers start: 32 outliers final: 15 residues processed: 118 average time/residue: 0.6657 time to fit residues: 85.0524 Evaluate side-chains 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 37 optimal weight: 10.0000 chunk 72 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN A 544 ASN H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.163852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137849 restraints weight = 15771.479| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.50 r_work: 0.3549 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3548 r_free = 0.3548 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5960 Z= 0.176 Angle : 0.614 8.805 8078 Z= 0.301 Chirality : 0.043 0.218 925 Planarity : 0.004 0.045 969 Dihedral : 6.962 65.322 1007 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.47 % Allowed : 24.28 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.79 (0.32), residues: 716 helix: 1.69 (0.27), residues: 346 sheet: 0.35 (0.54), residues: 102 loop : -0.95 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.021 0.001 TYR A 590 ARG 0.002 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 0.643 Fit side-chains REVERT: A 640 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7362 (t80) REVERT: H 21 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6987 (tp) REVERT: H 117 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.6463 (mpt) REVERT: L 48 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7200 (mt) REVERT: L 67 ARG cc_start: 0.6363 (OUTLIER) cc_final: 0.5780 (ppt170) outliers start: 28 outliers final: 14 residues processed: 113 average time/residue: 0.6958 time to fit residues: 85.0177 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 117 MET Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 14 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 3 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 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 = 0.3968 r_free = 0.3968 target = 0.164572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.138875 restraints weight = 23126.587| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.14 r_work: 0.3555 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3554 r_free = 0.3554 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5960 Z= 0.176 Angle : 0.626 8.261 8078 Z= 0.309 Chirality : 0.043 0.219 925 Planarity : 0.004 0.044 969 Dihedral : 6.801 58.175 1007 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.99 % Allowed : 25.40 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 4.35 % 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: 0.81 (0.32), residues: 716 helix: 1.72 (0.27), residues: 346 sheet: 0.39 (0.53), residues: 108 loop : -1.01 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.004 0.001 HIS A 520 PHE 0.012 0.001 PHE A 175 TYR 0.020 0.001 TYR A 590 ARG 0.004 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 103 time to evaluate : 0.647 Fit side-chains REVERT: A 640 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7361 (t80) REVERT: H 21 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6989 (tp) REVERT: L 48 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7197 (mt) REVERT: L 67 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5725 (ppt170) outliers start: 25 outliers final: 13 residues processed: 116 average time/residue: 0.8389 time to fit residues: 103.9822 Evaluate side-chains 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 5.9990 chunk 64 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140121 restraints weight = 21853.869| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.93 r_work: 0.3567 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5960 Z= 0.165 Angle : 0.612 7.889 8078 Z= 0.303 Chirality : 0.042 0.217 925 Planarity : 0.004 0.044 969 Dihedral : 6.353 59.047 1007 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.67 % Allowed : 27.48 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.85 (0.32), residues: 716 helix: 1.78 (0.28), residues: 347 sheet: 0.47 (0.54), residues: 102 loop : -1.04 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.021 0.001 TYR A 590 ARG 0.004 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.761 Fit side-chains REVERT: A 83 PHE cc_start: 0.6845 (m-10) cc_final: 0.6442 (m-80) REVERT: A 640 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7334 (t80) REVERT: H 21 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6940 (tp) REVERT: L 48 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7185 (mt) REVERT: L 67 ARG cc_start: 0.6312 (OUTLIER) cc_final: 0.5718 (ppt170) outliers start: 23 outliers final: 11 residues processed: 113 average time/residue: 0.7648 time to fit residues: 92.9864 Evaluate side-chains 111 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 19 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.138643 restraints weight = 21525.021| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.81 r_work: 0.3517 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3544 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3544 r_free = 0.3544 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3544 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5960 Z= 0.198 Angle : 0.631 7.983 8078 Z= 0.315 Chirality : 0.042 0.220 925 Planarity : 0.004 0.046 969 Dihedral : 6.308 59.622 1007 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.79 % Allowed : 25.56 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.76 (0.32), residues: 716 helix: 1.70 (0.28), residues: 347 sheet: 0.47 (0.54), residues: 102 loop : -1.10 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.003 0.001 HIS A 169 PHE 0.013 0.001 PHE A 175 TYR 0.019 0.001 TYR A 590 ARG 0.005 0.000 ARG A 580 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.651 Fit side-chains REVERT: A 83 PHE cc_start: 0.6918 (m-10) cc_final: 0.6554 (m-80) REVERT: A 180 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.6905 (mm) REVERT: A 596 ASP cc_start: 0.7635 (m-30) cc_final: 0.7387 (m-30) REVERT: A 640 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7320 (t80) REVERT: A 650 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8026 (mptm) REVERT: H 21 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6954 (tp) REVERT: L 48 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7237 (mt) outliers start: 30 outliers final: 17 residues processed: 119 average time/residue: 0.7775 time to fit residues: 99.2321 Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.141607 restraints weight = 25379.042| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.63 r_work: 0.3497 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5960 Z= 0.169 Angle : 0.614 8.269 8078 Z= 0.303 Chirality : 0.042 0.217 925 Planarity : 0.004 0.045 969 Dihedral : 5.970 59.095 1007 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.19 % Allowed : 27.32 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.84 (0.32), residues: 716 helix: 1.76 (0.28), residues: 347 sheet: 0.42 (0.53), residues: 107 loop : -1.03 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 169 PHE 0.013 0.001 PHE A 175 TYR 0.021 0.001 TYR A 590 ARG 0.004 0.000 ARG A 526 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.619 Fit side-chains REVERT: A 83 PHE cc_start: 0.6835 (m-10) cc_final: 0.6509 (m-80) REVERT: A 596 ASP cc_start: 0.7661 (m-30) cc_final: 0.7422 (m-30) REVERT: A 640 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7411 (t80) REVERT: A 650 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8010 (mptm) REVERT: H 21 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6932 (tp) REVERT: L 48 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7247 (mt) REVERT: L 67 ARG cc_start: 0.6371 (OUTLIER) cc_final: 0.5944 (ppt170) outliers start: 20 outliers final: 13 residues processed: 114 average time/residue: 0.7531 time to fit residues: 92.2289 Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 54 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.163901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.138020 restraints weight = 21065.178| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.84 r_work: 0.3513 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5960 Z= 0.209 Angle : 0.647 8.147 8078 Z= 0.323 Chirality : 0.043 0.222 925 Planarity : 0.004 0.046 969 Dihedral : 6.178 59.618 1007 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.99 % Allowed : 27.00 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.73 (0.32), residues: 716 helix: 1.66 (0.28), residues: 346 sheet: 0.45 (0.54), residues: 102 loop : -1.07 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.004 0.001 HIS A 169 PHE 0.013 0.001 PHE A 73 TYR 0.017 0.001 TYR A 590 ARG 0.004 0.000 ARG A 526 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1432 Ramachandran restraints generated. 716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.688 Fit side-chains REVERT: A 83 PHE cc_start: 0.6866 (m-10) cc_final: 0.6571 (m-80) REVERT: A 640 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7322 (t80) REVERT: A 650 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8009 (mptm) REVERT: H 21 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6905 (tp) REVERT: L 48 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.7224 (mt) REVERT: L 62 ARG cc_start: 0.6260 (tmm-80) cc_final: 0.5865 (tmm-80) outliers start: 25 outliers final: 17 residues processed: 115 average time/residue: 0.7735 time to fit residues: 95.6338 Evaluate side-chains 120 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 58 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 45 optimal weight: 0.0970 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 55 optimal weight: 0.0670 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN L 90 GLN L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.165614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139546 restraints weight = 20749.093| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 2.78 r_work: 0.3554 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3555 r_free = 0.3555 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5960 Z= 0.169 Angle : 0.617 8.154 8078 Z= 0.306 Chirality : 0.042 0.217 925 Planarity : 0.004 0.045 969 Dihedral : 5.939 58.350 1007 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.83 % Allowed : 27.00 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % 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: 0.81 (0.32), residues: 716 helix: 1.74 (0.28), residues: 346 sheet: 0.40 (0.52), residues: 108 loop : -1.04 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.004 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.021 0.001 TYR A 590 ARG 0.004 0.000 ARG A 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4347.23 seconds wall clock time: 75 minutes 1.29 seconds (4501.29 seconds total)