Starting phenix.real_space_refine on Fri Jul 19 02:49:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/07_2024/8pg0_17655.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/07_2024/8pg0_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/07_2024/8pg0_17655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/07_2024/8pg0_17655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/07_2024/8pg0_17655.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pg0_17655/07_2024/8pg0_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 Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A TYR 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 7.65, per 1000 atoms: 1.32 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 503 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.6 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: 0.58 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: 1.62 Time building geometry restraints manager: 2.62 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: 99.36 - 111.29: 2593 111.29 - 123.22: 5170 123.22 - 135.15: 314 135.15 - 147.08: 0 147.08 - 159.00: 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 2.440 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 2.440 nonbonded pdb=" O SER A 228 " pdb=" OG SER A 372 " model vdw 2.281 2.440 nonbonded pdb=" ND1 HIS A 115 " pdb=" O2 BCT A 802 " model vdw 2.299 2.520 ... (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 ========== 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: 5.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.310 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 24.450 Find NCS groups from input model: 0.050 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:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.760 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.564 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: 0.7874 time to fit residues: 90.2811 Evaluate side-chains 91 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 88 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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: 2.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5960 Z= 0.228 Angle : 0.656 8.863 8078 Z= 0.324 Chirality : 0.044 0.221 925 Planarity : 0.004 0.049 969 Dihedral : 7.931 80.873 1009 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.65 % Favored : 96.21 % Rotamer: Outliers : 5.11 % Allowed : 21.41 % Favored : 73.48 % 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: 1.73 (0.28), residues: 347 sheet: 0.12 (0.53), residues: 108 loop : -0.99 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.002 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.019 0.001 TYR A 590 ARG 0.003 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 132 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 0.627 Fit side-chains REVERT: A 390 MET cc_start: 0.6062 (OUTLIER) cc_final: 0.5812 (ptm) REVERT: A 446 ASN cc_start: 0.6092 (m-40) cc_final: 0.5873 (m-40) REVERT: A 640 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7458 (t80) REVERT: H 21 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7193 (tp) REVERT: L 67 ARG cc_start: 0.6286 (OUTLIER) cc_final: 0.5846 (ppt170) outliers start: 32 outliers final: 12 residues processed: 118 average time/residue: 0.6868 time to fit residues: 87.7132 Evaluate side-chains 104 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 390 MET Chi-restraints excluded: chain A residue 474 CYS 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 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 5960 Z= 0.359 Angle : 0.753 11.947 8078 Z= 0.372 Chirality : 0.048 0.243 925 Planarity : 0.005 0.046 969 Dihedral : 8.125 83.494 1007 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.59 % Allowed : 23.00 % Favored : 71.41 % 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: 0.37 (0.32), residues: 716 helix: 1.14 (0.28), residues: 353 sheet: 0.45 (0.55), residues: 94 loop : -1.00 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 254 HIS 0.003 0.001 HIS A 92 PHE 0.018 0.002 PHE A 73 TYR 0.016 0.002 TYR A 590 ARG 0.005 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 136 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 101 time to evaluate : 0.638 Fit side-chains REVERT: A 239 TYR cc_start: 0.6987 (m-10) cc_final: 0.5863 (m-10) REVERT: A 640 TYR cc_start: 0.8123 (OUTLIER) cc_final: 0.7492 (t80) REVERT: H 21 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7064 (tp) REVERT: H 114 ASP cc_start: 0.7872 (t0) cc_final: 0.6805 (t0) REVERT: H 117 MET cc_start: 0.7777 (OUTLIER) cc_final: 0.6596 (mpt) REVERT: L 48 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7370 (mt) REVERT: L 67 ARG cc_start: 0.6422 (OUTLIER) cc_final: 0.5979 (ppt170) outliers start: 35 outliers final: 20 residues processed: 117 average time/residue: 0.7147 time to fit residues: 90.0503 Evaluate side-chains 119 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 94 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 118 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 330 LYS 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 556 ILE 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 126 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 65 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1899 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= 0.180 Angle : 0.620 9.035 8078 Z= 0.302 Chirality : 0.043 0.219 925 Planarity : 0.004 0.045 969 Dihedral : 7.326 77.677 1007 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 5.43 % Allowed : 25.08 % 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: 0.72 (0.32), residues: 716 helix: 1.62 (0.28), residues: 345 sheet: 0.26 (0.52), residues: 107 loop : -0.95 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.003 0.001 HIS A 169 PHE 0.011 0.001 PHE A 175 TYR 0.024 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 140 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: A 239 TYR cc_start: 0.6969 (m-10) cc_final: 0.6012 (m-10) REVERT: A 640 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7445 (t80) REVERT: H 21 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6995 (tp) REVERT: H 117 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6566 (mpt) REVERT: L 67 ARG cc_start: 0.6381 (OUTLIER) cc_final: 0.5881 (ppt170) outliers start: 34 outliers final: 14 residues processed: 118 average time/residue: 0.8026 time to fit residues: 101.7166 Evaluate side-chains 116 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 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 332 ILE Chi-restraints excluded: chain A residue 448 VAL 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 H residue 51 VAL Chi-restraints excluded: chain H residue 117 MET 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 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: 0.6980 chunk 1 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 29 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN H 80 ASN L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5960 Z= 0.236 Angle : 0.658 9.092 8078 Z= 0.324 Chirality : 0.044 0.227 925 Planarity : 0.004 0.045 969 Dihedral : 7.402 69.780 1007 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.79 % Allowed : 25.88 % Favored : 69.33 % 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: 1.52 (0.28), residues: 345 sheet: 0.92 (0.55), residues: 92 loop : -0.98 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 254 HIS 0.003 0.001 HIS A 520 PHE 0.013 0.001 PHE A 73 TYR 0.020 0.001 TYR A 590 ARG 0.003 0.000 ARG A 580 *********************** 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 131 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 101 time to evaluate : 0.617 Fit side-chains revert: symmetry clash REVERT: A 239 TYR cc_start: 0.6997 (m-10) cc_final: 0.6016 (m-10) REVERT: A 390 MET cc_start: 0.6034 (pp-130) cc_final: 0.5643 (ptm) REVERT: A 640 TYR cc_start: 0.8015 (OUTLIER) cc_final: 0.7376 (t80) REVERT: H 21 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7024 (tp) REVERT: H 117 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.6642 (mpt) REVERT: L 48 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7258 (mt) REVERT: L 67 ARG cc_start: 0.6403 (OUTLIER) cc_final: 0.6079 (ppt170) outliers start: 30 outliers final: 19 residues processed: 117 average time/residue: 0.7538 time to fit residues: 94.6023 Evaluate side-chains 119 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 95 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 448 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 527 ASP 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 96 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 0.0020 chunk 13 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN L 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5960 Z= 0.189 Angle : 0.643 8.790 8078 Z= 0.319 Chirality : 0.044 0.221 925 Planarity : 0.004 0.045 969 Dihedral : 7.131 61.731 1007 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Rotamer: Outliers : 4.79 % Allowed : 25.72 % Favored : 69.49 % 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: 1.68 (0.28), residues: 345 sheet: 0.56 (0.53), residues: 107 loop : -1.01 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.004 0.001 HIS A 520 PHE 0.012 0.001 PHE A 175 TYR 0.022 0.001 TYR A 590 ARG 0.002 0.000 ARG A 526 *********************** 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 132 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 102 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 239 TYR cc_start: 0.7003 (m-80) cc_final: 0.6151 (m-10) REVERT: A 378 LEU cc_start: 0.8814 (mt) cc_final: 0.8530 (mt) REVERT: A 640 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7446 (t80) REVERT: A 650 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8065 (mptm) REVERT: H 21 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6967 (tp) REVERT: L 48 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7245 (mt) REVERT: L 67 ARG cc_start: 0.6317 (OUTLIER) cc_final: 0.6043 (ppt170) outliers start: 30 outliers final: 17 residues processed: 119 average time/residue: 0.8701 time to fit residues: 110.6857 Evaluate side-chains 117 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 95 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 477 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 527 ASP 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 H residue 126 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN L 7 GLN L 90 GLN L 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5960 Z= 0.165 Angle : 0.611 8.068 8078 Z= 0.304 Chirality : 0.042 0.217 925 Planarity : 0.004 0.045 969 Dihedral : 6.586 58.603 1007 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.63 % Allowed : 26.68 % Favored : 68.69 % 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: 0.92 (0.32), residues: 716 helix: 1.82 (0.28), residues: 345 sheet: 0.59 (0.53), residues: 107 loop : -1.02 (0.39), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 PHE 0.013 0.001 PHE A 175 TYR 0.023 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 129 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 100 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7050 (m-10) cc_final: 0.6693 (m-80) REVERT: A 239 TYR cc_start: 0.6967 (m-80) cc_final: 0.6240 (m-10) REVERT: A 640 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.7466 (t80) REVERT: A 650 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8063 (mptm) REVERT: H 21 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6964 (tp) REVERT: L 48 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7209 (mt) REVERT: L 67 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.5856 (ppt170) outliers start: 29 outliers final: 13 residues processed: 119 average time/residue: 0.7765 time to fit residues: 99.5744 Evaluate side-chains 112 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.673 ------------------------------------------------------------------------------- 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 477 ASN 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 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 97 ILE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 64 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.2277 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= 0.211 Angle : 0.644 8.246 8078 Z= 0.319 Chirality : 0.043 0.224 925 Planarity : 0.004 0.046 969 Dihedral : 6.649 59.710 1007 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.31 % Allowed : 27.00 % Favored : 68.69 % 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: 0.78 (0.33), residues: 716 helix: 1.68 (0.28), residues: 346 sheet: 0.48 (0.53), residues: 107 loop : -1.06 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 PHE 0.013 0.001 PHE A 73 TYR 0.020 0.001 TYR A 590 ARG 0.003 0.000 ARG A 526 *********************** 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 127 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7117 (m-10) cc_final: 0.6800 (m-80) REVERT: A 390 MET cc_start: 0.5987 (pp-130) cc_final: 0.5596 (ptm) REVERT: A 640 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.7391 (t80) REVERT: A 650 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8095 (mptm) REVERT: H 21 LEU cc_start: 0.7330 (OUTLIER) cc_final: 0.6994 (tp) REVERT: L 48 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7266 (mt) outliers start: 27 outliers final: 19 residues processed: 116 average time/residue: 0.8229 time to fit residues: 102.5665 Evaluate side-chains 118 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 477 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 527 ASP 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 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 H residue 126 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 42 optimal weight: 0.0870 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5960 Z= 0.189 Angle : 0.627 8.183 8078 Z= 0.311 Chirality : 0.042 0.221 925 Planarity : 0.004 0.045 969 Dihedral : 6.369 59.660 1007 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 4.15 % Allowed : 27.32 % Favored : 68.53 % 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: 0.80 (0.33), residues: 716 helix: 1.71 (0.28), residues: 346 sheet: 0.46 (0.53), residues: 107 loop : -1.05 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 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 fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.7066 (m-10) cc_final: 0.6758 (m-80) REVERT: A 378 LEU cc_start: 0.8834 (mt) cc_final: 0.8560 (mt) REVERT: A 390 MET cc_start: 0.5993 (pp-130) cc_final: 0.5520 (ptm) REVERT: A 640 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7367 (t80) REVERT: A 650 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8114 (mptm) REVERT: H 21 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6963 (tp) REVERT: L 48 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7246 (mt) outliers start: 26 outliers final: 19 residues processed: 113 average time/residue: 0.7352 time to fit residues: 89.3633 Evaluate side-chains 116 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 477 ASN Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 527 ASP 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 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 H residue 126 THR 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 32 optimal weight: 0.0970 chunk 48 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.2321 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= 0.161 Angle : 0.603 8.138 8078 Z= 0.298 Chirality : 0.042 0.216 925 Planarity : 0.004 0.045 969 Dihedral : 6.119 58.997 1007 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.35 % Allowed : 28.59 % Favored : 68.05 % 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: 0.91 (0.33), residues: 716 helix: 1.82 (0.28), residues: 346 sheet: 0.49 (0.53), residues: 107 loop : -1.00 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.024 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 117 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6974 (m-10) cc_final: 0.6706 (m-80) REVERT: A 390 MET cc_start: 0.6012 (pp-130) cc_final: 0.5678 (ptm) REVERT: A 596 ASP cc_start: 0.7840 (m-30) cc_final: 0.7619 (m-30) REVERT: A 640 TYR cc_start: 0.7849 (OUTLIER) cc_final: 0.7440 (t80) REVERT: A 650 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8073 (mptm) REVERT: H 21 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6933 (tp) REVERT: L 48 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7192 (mt) REVERT: L 67 ARG cc_start: 0.6287 (OUTLIER) cc_final: 0.5863 (ppt170) outliers start: 21 outliers final: 13 residues processed: 109 average time/residue: 0.6980 time to fit residues: 82.0635 Evaluate side-chains 113 residues out of total 624 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 95 time to evaluate : 0.644 ------------------------------------------------------------------------------- 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 527 ASP 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 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 126 THR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.0060 chunk 58 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.166384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.140432 restraints weight = 19637.179| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.63 r_work: 0.3522 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3539 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3539 r_free = 0.3539 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 = 0.3539 r_free = 0.3539 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3539 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2383 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= 0.162 Angle : 0.595 8.100 8078 Z= 0.296 Chirality : 0.041 0.218 925 Planarity : 0.004 0.045 969 Dihedral : 5.964 58.691 1007 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.19 % Allowed : 28.91 % Favored : 67.89 % 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: 0.96 (0.33), residues: 716 helix: 1.88 (0.28), residues: 346 sheet: 0.44 (0.53), residues: 107 loop : -0.97 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.004 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.022 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: 2501.04 seconds wall clock time: 44 minutes 39.39 seconds (2679.39 seconds total)