Starting phenix.real_space_refine on Thu Jul 2 02:41:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pg0_17655/07_2026/8pg0_17655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pg0_17655/07_2026/8pg0_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8pg0_17655/07_2026/8pg0_17655.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pg0_17655/07_2026/8pg0_17655.cif" model { file = "/net/cci-nas-00/data/ceres_data/8pg0_17655/07_2026/8pg0_17655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pg0_17655/07_2026/8pg0_17655.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pg0_17655/07_2026/8pg0_17655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pg0_17655/07_2026/8pg0_17655.map" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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: 1.40, per 1000 atoms: 0.24 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: 0.29 Conformation dependent library (CDL) restraints added in 279.8 milliseconds 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: 0.13 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: 0.62 Time building geometry restraints manager: 0.39 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 - 22.08: 3112 22.08 - 44.16: 261 44.16 - 66.23: 46 66.23 - 88.31: 4 88.31 - 110.39: 1 Dihedral angle restraints: 3424 sinusoidal: 1322 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 3421 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: 5.880 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: 0.190 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.060 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:5.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 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 5969 Z= 1.552 Angle : 0.948 37.304 8097 Z= 0.587 Chirality : 0.058 0.416 925 Planarity : 0.009 0.228 969 Dihedral : 15.887 110.387 2062 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.003 0.000 ARG A 181 TYR 0.018 0.001 TYR A 590 PHE 0.011 0.001 PHE A 175 TRP 0.010 0.001 TRP H 50 HIS 0.002 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.02177 / 1.55 ( 5960) covalent geometry : angle 0.94257 / 0.59 ( 8078) SS BOND : bond 0.00460 / 0.32 ( 8) SS BOND : angle 0.55445 / 0.33 ( 16) hydrogen bonds : bond 0.16849 / 10.90 ( 327) hydrogen bonds : angle 6.63758 / 4.77 ( 946) link_NAG-ASN : bond 0.07217 / 4.51 ( 1) link_NAG-ASN : angle 5.68672 / 3.02 ( 3) *********************** 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 : 0.131 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: 0.2521 time to fit residues: 28.7713 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 : 0.126 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3964 r_free = 0.3964 target = 0.164201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.138061 restraints weight = 20380.957| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.81 r_work: 0.3529 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5969 Z= 0.153 Angle : 0.640 8.876 8097 Z= 0.318 Chirality : 0.045 0.313 925 Planarity : 0.004 0.048 969 Dihedral : 6.787 107.183 820 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 9.67 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.32), residues: 716 helix: 1.63 (0.27), residues: 353 sheet: 0.06 (0.53), residues: 108 loop : -0.96 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.020 0.001 TYR A 590 PHE 0.011 0.001 PHE A 175 TRP 0.007 0.001 TRP A 254 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 5960) covalent geometry : angle 0.63959 / 0.32 ( 8078) SS BOND : bond 0.00330 / 0.24 ( 8) SS BOND : angle 0.80188 / 0.52 ( 16) hydrogen bonds : bond 0.04839 / 3.16 ( 327) hydrogen bonds : angle 4.99491 / 3.75 ( 946) link_NAG-ASN : bond 0.00946 / 0.59 ( 1) link_NAG-ASN : angle 0.69224 / 0.35 ( 3) *********************** 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 128 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.141 Fit side-chains REVERT: A 390 MET cc_start: 0.6207 (OUTLIER) cc_final: 0.5798 (ptm) REVERT: A 446 ASN cc_start: 0.6101 (m-40) cc_final: 0.5890 (m-40) REVERT: A 640 TYR cc_start: 0.7923 (OUTLIER) cc_final: 0.7304 (t80) REVERT: H 21 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7254 (tp) REVERT: L 67 ARG cc_start: 0.6302 (OUTLIER) cc_final: 0.5846 (ppt170) outliers start: 30 outliers final: 10 residues processed: 115 average time/residue: 0.2188 time to fit residues: 27.2937 Evaluate side-chains 101 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.136 ------------------------------------------------------------------------------- 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 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 43 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 7 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.164503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.138718 restraints weight = 21715.364| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.02 r_work: 0.3580 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5969 Z= 0.125 Angle : 0.606 12.322 8097 Z= 0.296 Chirality : 0.043 0.260 925 Planarity : 0.004 0.044 969 Dihedral : 6.433 106.429 818 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 5.11 % Allowed : 23.00 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.32), residues: 716 helix: 1.86 (0.27), residues: 346 sheet: 0.04 (0.51), residues: 110 loop : -0.92 (0.40), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.021 0.001 TYR A 590 PHE 0.011 0.001 PHE A 175 TRP 0.006 0.001 TRP H 50 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5960) covalent geometry : angle 0.60617 / 0.30 ( 8078) SS BOND : bond 0.00259 / 0.18 ( 8) SS BOND : angle 0.66906 / 0.43 ( 16) hydrogen bonds : bond 0.04310 / 2.84 ( 327) hydrogen bonds : angle 4.66417 / 3.52 ( 946) link_NAG-ASN : bond 0.00617 / 0.39 ( 1) link_NAG-ASN : angle 1.00022 / 0.46 ( 3) *********************** 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 131 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.166 Fit side-chains REVERT: A 239 TYR cc_start: 0.6887 (m-10) cc_final: 0.5918 (m-10) REVERT: A 446 ASN cc_start: 0.6308 (m-40) cc_final: 0.6093 (m-40) REVERT: A 577 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7930 (tmt) REVERT: A 640 TYR cc_start: 0.7915 (OUTLIER) cc_final: 0.7395 (t80) REVERT: H 21 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7058 (tp) REVERT: L 48 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6976 (mt) REVERT: L 67 ARG cc_start: 0.6354 (OUTLIER) cc_final: 0.5875 (ppt170) outliers start: 32 outliers final: 12 residues processed: 116 average time/residue: 0.2632 time to fit residues: 32.7763 Evaluate side-chains 106 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 465 CYS Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 577 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 39 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 29 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3974 r_free = 0.3974 target = 0.164790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.138981 restraints weight = 17654.473| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.53 r_work: 0.3538 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3545 r_free = 0.3545 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 = 0.3545 r_free = 0.3545 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5969 Z= 0.129 Angle : 0.608 8.966 8097 Z= 0.298 Chirality : 0.043 0.255 925 Planarity : 0.004 0.044 969 Dihedral : 6.440 106.253 818 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.67 % Allowed : 24.76 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.32), residues: 716 helix: 1.83 (0.28), residues: 346 sheet: 0.17 (0.51), residues: 113 loop : -0.88 (0.40), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.020 0.001 TYR A 590 PHE 0.012 0.001 PHE A 175 TRP 0.006 0.001 TRP A 254 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 5960) covalent geometry : angle 0.60736 / 0.30 ( 8078) SS BOND : bond 0.00275 / 0.20 ( 8) SS BOND : angle 0.69352 / 0.41 ( 16) hydrogen bonds : bond 0.04282 / 2.81 ( 327) hydrogen bonds : angle 4.57772 / 3.47 ( 946) link_NAG-ASN : bond 0.00635 / 0.40 ( 1) link_NAG-ASN : angle 0.84297 / 0.39 ( 3) *********************** 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 122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.169 Fit side-chains REVERT: A 239 TYR cc_start: 0.6977 (m-10) cc_final: 0.6139 (m-10) REVERT: A 390 MET cc_start: 0.6169 (pp-130) cc_final: 0.5647 (ptm) REVERT: A 446 ASN cc_start: 0.6405 (m-40) cc_final: 0.6190 (m-40) REVERT: A 577 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7931 (tmt) REVERT: A 640 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7348 (t80) REVERT: H 21 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7043 (tp) REVERT: L 48 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7102 (mt) REVERT: L 67 ARG cc_start: 0.6285 (OUTLIER) cc_final: 0.5798 (ppt170) outliers start: 23 outliers final: 12 residues processed: 111 average time/residue: 0.2882 time to fit residues: 34.2692 Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.213 ------------------------------------------------------------------------------- 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 411 SER 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 563 VAL Chi-restraints excluded: chain A residue 577 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 22 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3957 r_free = 0.3957 target = 0.163435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.137927 restraints weight = 14603.617| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.32 r_work: 0.3508 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5969 Z= 0.148 Angle : 0.646 8.535 8097 Z= 0.322 Chirality : 0.044 0.265 925 Planarity : 0.004 0.046 969 Dihedral : 6.651 106.048 818 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 9.33 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 : 4.35 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.32), residues: 716 helix: 1.70 (0.28), residues: 346 sheet: 0.36 (0.54), residues: 102 loop : -1.06 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 62 TYR 0.017 0.001 TYR A 590 PHE 0.012 0.001 PHE A 175 TRP 0.005 0.001 TRP A 254 HIS 0.003 0.001 HIS A 520 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 5960) covalent geometry : angle 0.63789 / 0.32 ( 8078) SS BOND : bond 0.00518 / 0.36 ( 8) SS BOND : angle 2.29940 / 2.20 ( 16) hydrogen bonds : bond 0.04563 / 2.96 ( 327) hydrogen bonds : angle 4.63894 / 3.54 ( 946) link_NAG-ASN : bond 0.00620 / 0.39 ( 1) link_NAG-ASN : angle 0.91716 / 0.43 ( 3) *********************** 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 : 0.131 Fit side-chains REVERT: A 446 ASN cc_start: 0.6542 (m-40) cc_final: 0.6251 (m110) REVERT: A 640 TYR cc_start: 0.7948 (OUTLIER) cc_final: 0.7296 (t80) REVERT: H 21 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7042 (tp) REVERT: L 48 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7211 (mt) REVERT: L 67 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5781 (ppt170) outliers start: 28 outliers final: 15 residues processed: 112 average time/residue: 0.3082 time to fit residues: 36.7139 Evaluate side-chains 111 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 43 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 9 optimal weight: 0.3980 chunk 72 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3989 r_free = 0.3989 target = 0.166219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140355 restraints weight = 23363.417| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 3.34 r_work: 0.3568 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3566 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3566 r_free = 0.3566 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3566 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.003 0.031 5969 Z= 0.121 Angle : 0.605 8.016 8097 Z= 0.300 Chirality : 0.043 0.251 925 Planarity : 0.004 0.045 969 Dihedral : 6.455 106.076 818 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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 : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.32), residues: 716 helix: 1.82 (0.28), residues: 346 sheet: 0.40 (0.53), residues: 107 loop : -1.02 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 526 TYR 0.021 0.001 TYR A 590 PHE 0.011 0.001 PHE A 175 TRP 0.007 0.001 TRP A 470 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 5960) covalent geometry : angle 0.60118 / 0.30 ( 8078) SS BOND : bond 0.00363 / 0.26 ( 8) SS BOND : angle 1.70581 / 1.54 ( 16) hydrogen bonds : bond 0.04078 / 2.69 ( 327) hydrogen bonds : angle 4.48123 / 3.41 ( 946) link_NAG-ASN : bond 0.00631 / 0.39 ( 1) link_NAG-ASN : angle 0.80079 / 0.37 ( 3) *********************** 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 127 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.151 Fit side-chains REVERT: A 446 ASN cc_start: 0.6388 (m-40) cc_final: 0.6135 (m110) REVERT: A 640 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7329 (t80) REVERT: H 21 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6978 (tp) REVERT: L 48 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7135 (mt) REVERT: L 67 ARG cc_start: 0.6252 (OUTLIER) cc_final: 0.5693 (ppt170) outliers start: 25 outliers final: 14 residues processed: 114 average time/residue: 0.3081 time to fit residues: 37.4743 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.165 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 64 optimal weight: 0.1980 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 63 optimal weight: 0.0870 chunk 34 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4039 r_free = 0.4039 target = 0.170858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.144971 restraints weight = 21782.278| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.12 r_work: 0.3632 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3630 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5969 Z= 0.106 Angle : 0.581 7.754 8097 Z= 0.286 Chirality : 0.042 0.231 925 Planarity : 0.004 0.044 969 Dihedral : 6.280 106.249 818 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.35 % Allowed : 27.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.32), residues: 716 helix: 1.99 (0.28), residues: 346 sheet: 0.57 (0.52), residues: 111 loop : -1.02 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 580 TYR 0.023 0.001 TYR A 590 PHE 0.012 0.001 PHE A 175 TRP 0.011 0.001 TRP A 470 HIS 0.002 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 5960) covalent geometry : angle 0.57826 / 0.29 ( 8078) SS BOND : bond 0.00261 / 0.17 ( 8) SS BOND : angle 1.32677 / 1.11 ( 16) hydrogen bonds : bond 0.03588 / 2.39 ( 327) hydrogen bonds : angle 4.27674 / 3.22 ( 946) link_NAG-ASN : bond 0.00588 / 0.37 ( 1) link_NAG-ASN : angle 0.64947 / 0.32 ( 3) *********************** 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 130 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.222 Fit side-chains REVERT: A 83 PHE cc_start: 0.6666 (m-10) cc_final: 0.6265 (m-80) REVERT: A 446 ASN cc_start: 0.6326 (m-40) cc_final: 0.6102 (m110) REVERT: H 21 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7023 (tp) REVERT: L 48 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7126 (mt) outliers start: 21 outliers final: 10 residues processed: 118 average time/residue: 0.2527 time to fit residues: 32.2507 Evaluate side-chains 104 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.167 ------------------------------------------------------------------------------- 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 411 SER Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 60 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 0.0030 chunk 24 optimal weight: 0.9990 overall best weight: 1.0394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.164780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.138634 restraints weight = 21096.313| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 3.00 r_work: 0.3547 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 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 = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 5969 Z= 0.139 Angle : 0.632 7.950 8097 Z= 0.314 Chirality : 0.043 0.263 925 Planarity : 0.004 0.046 969 Dihedral : 6.226 106.007 816 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.15 % Allowed : 26.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.32), residues: 716 helix: 1.82 (0.28), residues: 347 sheet: 0.50 (0.52), residues: 108 loop : -1.07 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 580 TYR 0.018 0.001 TYR A 590 PHE 0.014 0.001 PHE A 73 TRP 0.005 0.001 TRP A 254 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5960) covalent geometry : angle 0.62976 / 0.31 ( 8078) SS BOND : bond 0.00446 / 0.32 ( 8) SS BOND : angle 1.31685 / 1.17 ( 16) hydrogen bonds : bond 0.04352 / 2.85 ( 327) hydrogen bonds : angle 4.52787 / 3.44 ( 946) link_NAG-ASN : bond 0.00639 / 0.40 ( 1) link_NAG-ASN : angle 0.93427 / 0.43 ( 3) *********************** 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 122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6880 (m-10) cc_final: 0.6521 (m-80) REVERT: A 180 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.6859 (mm) REVERT: A 645 PHE cc_start: 0.7695 (t80) cc_final: 0.7493 (t80) REVERT: H 21 LEU cc_start: 0.7392 (OUTLIER) cc_final: 0.7043 (tp) REVERT: L 48 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7201 (mt) outliers start: 26 outliers final: 15 residues processed: 113 average time/residue: 0.2469 time to fit residues: 30.0885 Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.171 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 248 THR 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 548 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 648 LYS Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 11 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3979 r_free = 0.3979 target = 0.165383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.140209 restraints weight = 15733.163| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.43 r_work: 0.3569 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3569 r_free = 0.3569 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5969 Z= 0.128 Angle : 0.623 7.955 8097 Z= 0.307 Chirality : 0.043 0.255 925 Planarity : 0.004 0.045 969 Dihedral : 6.200 106.080 816 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.67 % Allowed : 27.80 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.32), residues: 716 helix: 1.78 (0.28), residues: 347 sheet: 0.50 (0.53), residues: 108 loop : -1.02 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 580 TYR 0.019 0.001 TYR A 590 PHE 0.012 0.001 PHE A 73 TRP 0.006 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 5960) covalent geometry : angle 0.62099 / 0.31 ( 8078) SS BOND : bond 0.00380 / 0.27 ( 8) SS BOND : angle 1.20021 / 1.04 ( 16) hydrogen bonds : bond 0.04159 / 2.73 ( 327) hydrogen bonds : angle 4.49597 / 3.41 ( 946) link_NAG-ASN : bond 0.00621 / 0.39 ( 1) link_NAG-ASN : angle 0.90958 / 0.42 ( 3) *********************** 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: 23 poor density : 98 time to evaluate : 0.145 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6848 (m-10) cc_final: 0.6517 (m-80) REVERT: H 21 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7013 (tp) REVERT: L 48 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7215 (mt) outliers start: 23 outliers final: 16 residues processed: 111 average time/residue: 0.2532 time to fit residues: 30.1663 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.131 ------------------------------------------------------------------------------- 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 411 SER Chi-restraints excluded: chain A residue 448 VAL 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 580 ARG Chi-restraints excluded: chain A residue 648 LYS 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 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 64 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 544 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.163075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.136933 restraints weight = 20273.727| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.88 r_work: 0.3549 rms_B_bonded: 3.21 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 = 0.42 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5969 Z= 0.149 Angle : 0.649 8.075 8097 Z= 0.323 Chirality : 0.044 0.266 925 Planarity : 0.004 0.046 969 Dihedral : 6.318 106.144 816 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.83 % Allowed : 27.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.32), residues: 716 helix: 1.67 (0.28), residues: 347 sheet: 0.45 (0.53), residues: 108 loop : -1.08 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 62 TYR 0.016 0.001 TYR A 590 PHE 0.015 0.001 PHE A 73 TRP 0.008 0.001 TRP H 50 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 5960) covalent geometry : angle 0.64754 / 0.32 ( 8078) SS BOND : bond 0.00390 / 0.28 ( 8) SS BOND : angle 1.24745 / 1.09 ( 16) hydrogen bonds : bond 0.04500 / 2.94 ( 327) hydrogen bonds : angle 4.59518 / 3.50 ( 946) link_NAG-ASN : bond 0.00631 / 0.39 ( 1) link_NAG-ASN : angle 0.98640 / 0.45 ( 3) ********************** 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 to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6912 (m-10) cc_final: 0.6606 (m-80) REVERT: A 180 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.6893 (mm) REVERT: H 21 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6975 (tp) REVERT: L 48 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7225 (mt) outliers start: 24 outliers final: 16 residues processed: 108 average time/residue: 0.2470 time to fit residues: 28.8070 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 : 0.142 ------------------------------------------------------------------------------- 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 180 LEU Chi-restraints excluded: chain A residue 248 THR 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 548 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 648 LYS 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 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 55 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 64 optimal weight: 0.0020 chunk 6 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.5126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.167041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141122 restraints weight = 18690.727| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.64 r_work: 0.3599 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5969 Z= 0.117 Angle : 0.607 7.831 8097 Z= 0.300 Chirality : 0.042 0.244 925 Planarity : 0.004 0.045 969 Dihedral : 6.167 105.633 816 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.88 % Allowed : 28.75 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.32), residues: 716 helix: 1.77 (0.28), residues: 347 sheet: 0.45 (0.53), residues: 108 loop : -1.06 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 580 TYR 0.022 0.001 TYR A 590 PHE 0.011 0.001 PHE A 175 TRP 0.008 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 ( 5960) covalent geometry : angle 0.60508 / 0.30 ( 8078) SS BOND : bond 0.00403 / 0.29 ( 8) SS BOND : angle 1.15218 / 0.95 ( 16) hydrogen bonds : bond 0.03975 / 2.64 ( 327) hydrogen bonds : angle 4.45091 / 3.37 ( 946) link_NAG-ASN : bond 0.00602 / 0.38 ( 1) link_NAG-ASN : angle 0.85566 / 0.41 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1674.73 seconds wall clock time: 29 minutes 18.95 seconds (1758.95 seconds total)