Starting phenix.real_space_refine on Sun Apr 27 14:58:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pg0_17655/04_2025/8pg0_17655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pg0_17655/04_2025/8pg0_17655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8pg0_17655/04_2025/8pg0_17655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pg0_17655/04_2025/8pg0_17655.map" model { file = "/net/cci-nas-00/data/ceres_data/8pg0_17655/04_2025/8pg0_17655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pg0_17655/04_2025/8pg0_17655.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 3826 2.51 5 N 912 2.21 5 O 1040 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 7.40, per 1000 atoms: 1.27 Number of scatterers: 5816 At special positions: 0 Unit cell: (78.03, 119.85, 104.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 38 16.00 O 1040 8.00 N 912 7.00 C 3826 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.04 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 801 " - " ASN A 503 " Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 1.2 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: 1.86 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.56: 5900 1.56 - 1.91: 59 1.91 - 2.25: 0 2.25 - 2.60: 0 2.60 - 2.95: 1 Bond restraints: 5960 Sorted by residual: bond pdb=" C TYR L 50 " pdb=" N SER L 53 " ideal model delta sigma weight residual 1.329 2.947 -1.618 1.40e-02 5.10e+03 1.34e+04 bond pdb=" C ARG A 526 " pdb=" N ASP A 527 " ideal model delta sigma weight residual 1.328 1.432 -0.104 1.44e-02 4.82e+03 5.20e+01 bond pdb=" C VAL A 221 " pdb=" N ILE A 222 " ideal model delta sigma weight residual 1.335 1.282 0.053 1.26e-02 6.30e+03 1.77e+01 bond pdb=" N VAL A 563 " pdb=" CA VAL A 563 " ideal model delta sigma weight residual 1.456 1.494 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N GLY A 475 " pdb=" CA GLY A 475 " ideal model delta sigma weight residual 1.444 1.476 -0.031 1.06e-02 8.90e+03 8.83e+00 ... (remaining 5955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.46: 8074 7.46 - 14.92: 3 14.92 - 22.38: 0 22.38 - 29.84: 0 29.84 - 37.30: 1 Bond angle restraints: 8078 Sorted by residual: angle pdb=" C TYR L 50 " pdb=" N SER L 53 " pdb=" CA SER L 53 " ideal model delta sigma weight residual 121.70 159.00 -37.30 1.80e+00 3.09e-01 4.30e+02 angle pdb=" N ILE A 562 " pdb=" CA ILE A 562 " pdb=" C ILE A 562 " ideal model delta sigma weight residual 112.29 107.96 4.33 9.40e-01 1.13e+00 2.12e+01 angle pdb=" C SER L 10 " pdb=" CA SER L 10 " pdb=" CB SER L 10 " ideal model delta sigma weight residual 117.23 111.69 5.54 1.36e+00 5.41e-01 1.66e+01 angle pdb=" N ASN A 477 " pdb=" CA ASN A 477 " pdb=" C ASN A 477 " ideal model delta sigma weight residual 113.19 108.58 4.61 1.19e+00 7.06e-01 1.50e+01 angle pdb=" N ASN A 476 " pdb=" CA ASN A 476 " pdb=" C ASN A 476 " ideal model delta sigma weight residual 112.87 108.30 4.57 1.20e+00 6.94e-01 1.45e+01 ... (remaining 8073 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 3323 24.23 - 48.45: 246 48.45 - 72.68: 36 72.68 - 96.90: 5 96.90 - 121.13: 3 Dihedral angle restraints: 3613 sinusoidal: 1511 harmonic: 2102 Sorted by residual: dihedral pdb=" CA TYR L 50 " pdb=" C TYR L 50 " pdb=" N SER L 53 " pdb=" CA SER L 53 " ideal model delta harmonic sigma weight residual 0.00 -38.47 38.47 0 5.00e+00 4.00e-02 5.92e+01 dihedral pdb=" CB CYS A 459 " pdb=" SG CYS A 459 " pdb=" SG CYS A 506 " pdb=" CB CYS A 506 " ideal model delta sinusoidal sigma weight residual 93.00 131.42 -38.42 1 1.00e+01 1.00e-02 2.08e+01 dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 524 " pdb=" CB CYS A 524 " ideal model delta sinusoidal sigma weight residual 93.00 55.20 37.80 1 1.00e+01 1.00e-02 2.01e+01 ... (remaining 3610 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 795 0.083 - 0.166: 109 0.166 - 0.250: 19 0.250 - 0.333: 1 0.333 - 0.416: 1 Chirality restraints: 925 Sorted by residual: chirality pdb=" C1 NAG A 801 " pdb=" ND2 ASN A 503 " pdb=" C2 NAG A 801 " pdb=" O5 NAG A 801 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" C13 CLR A 805 " pdb=" C12 CLR A 805 " pdb=" C14 CLR A 805 " pdb=" C17 CLR A 805 " both_signs ideal model delta sigma weight residual False -2.93 -2.65 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C14 CLR A 805 " pdb=" C13 CLR A 805 " pdb=" C15 CLR A 805 " pdb=" C8 CLR A 805 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 922 not shown) Planarity restraints: 970 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 801 " 0.270 2.00e-02 2.50e+03 2.28e-01 6.47e+02 pdb=" C7 NAG A 801 " -0.069 2.00e-02 2.50e+03 pdb=" C8 NAG A 801 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG A 801 " -0.387 2.00e-02 2.50e+03 pdb=" O7 NAG A 801 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR L 50 " 0.023 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C TYR L 50 " -0.069 2.00e-02 2.50e+03 pdb=" O TYR L 50 " 0.032 2.00e-02 2.50e+03 pdb=" N SER L 53 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 471 " 0.053 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A 472 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 472 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 472 " 0.043 5.00e-02 4.00e+02 ... (remaining 967 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 586 2.75 - 3.29: 6007 3.29 - 3.82: 9912 3.82 - 4.36: 12040 4.36 - 4.90: 20237 Nonbonded interactions: 48782 Sorted by model distance: nonbonded pdb=" OE1 GLN A 366 " pdb=" OG SER A 618 " model vdw 2.211 3.040 nonbonded pdb=" O PRO A 472 " pdb=" O LEU A 521 " model vdw 2.252 3.040 nonbonded pdb=" O SER H 33 " pdb=" OG SER H 57 " model vdw 2.280 3.040 nonbonded pdb=" O SER A 228 " pdb=" OG SER A 372 " model vdw 2.281 3.040 nonbonded pdb=" ND1 HIS A 115 " pdb=" O2 BCT A 802 " model vdw 2.299 3.120 ... (remaining 48777 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.42 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.620 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: 0.370 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.610 Find NCS groups from input model: 0.060 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:14.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.830 ------------------------------------------------------------------------------- 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 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 : 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 Details of bonding type rmsd link_NAG-ASN : bond 0.07217 ( 1) link_NAG-ASN : angle 5.68672 ( 3) hydrogen bonds : bond 0.16849 ( 327) hydrogen bonds : angle 6.63758 ( 946) SS BOND : bond 0.00460 ( 8) SS BOND : angle 0.55445 ( 16) covalent geometry : bond 0.02177 ( 5960) covalent geometry : angle 0.94257 ( 8078) *********************** 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 : 0.691 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: 0.8155 time to fit residues: 93.3947 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 : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain L residue 55 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN A 476 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.166314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140470 restraints weight = 21606.302| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.91 r_work: 0.3556 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3558 r_free = 0.3558 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 = 0.3558 r_free = 0.3558 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5969 Z= 0.136 Angle : 0.639 9.485 8097 Z= 0.311 Chirality : 0.044 0.218 925 Planarity : 0.004 0.046 969 Dihedral : 7.611 77.457 1009 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.81 % Favored : 97.05 % Rotamer: Outliers : 4.15 % Allowed : 22.52 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.32), residues: 716 helix: 1.74 (0.27), residues: 352 sheet: 0.05 (0.53), residues: 108 loop : -0.96 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.002 0.001 HIS A 169 PHE 0.011 0.001 PHE A 175 TYR 0.022 0.001 TYR A 590 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00736 ( 1) link_NAG-ASN : angle 4.15146 ( 3) hydrogen bonds : bond 0.04444 ( 327) hydrogen bonds : angle 4.89338 ( 946) SS BOND : bond 0.00297 ( 8) SS BOND : angle 0.74249 ( 16) covalent geometry : bond 0.00292 ( 5960) covalent geometry : angle 0.63338 ( 8078) *********************** 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: 26 poor density : 102 time to evaluate : 0.667 Fit side-chains REVERT: A 390 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5885 (ptm) REVERT: A 446 ASN cc_start: 0.6094 (m-40) cc_final: 0.5881 (m-40) REVERT: A 640 TYR cc_start: 0.7863 (OUTLIER) cc_final: 0.7361 (t80) REVERT: H 21 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7270 (tp) REVERT: L 67 ARG cc_start: 0.6291 (OUTLIER) cc_final: 0.5827 (ppt170) outliers start: 26 outliers final: 8 residues processed: 117 average time/residue: 0.6729 time to fit residues: 85.2182 Evaluate side-chains 100 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 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 67 ARG Chi-restraints excluded: chain L residue 97 ILE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.162906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.137221 restraints weight = 20292.944| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 2.87 r_work: 0.3506 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3502 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3502 r_free = 0.3502 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 = 0.3502 r_free = 0.3502 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5969 Z= 0.156 Angle : 0.660 12.718 8097 Z= 0.320 Chirality : 0.044 0.219 925 Planarity : 0.004 0.045 969 Dihedral : 7.323 76.982 1007 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.59 % Allowed : 22.20 % Favored : 72.20 % 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: 1.58 (0.28), residues: 353 sheet: 0.15 (0.53), residues: 105 loop : -0.88 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.002 0.001 HIS A 169 PHE 0.012 0.001 PHE A 73 TYR 0.018 0.001 TYR A 590 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00015 ( 1) link_NAG-ASN : angle 3.52865 ( 3) hydrogen bonds : bond 0.04801 ( 327) hydrogen bonds : angle 4.82494 ( 946) SS BOND : bond 0.00296 ( 8) SS BOND : angle 0.76527 ( 16) covalent geometry : bond 0.00355 ( 5960) covalent geometry : angle 0.65659 ( 8078) *********************** 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 to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.679 Fit side-chains REVERT: A 446 ASN cc_start: 0.6392 (m-40) cc_final: 0.6180 (m-40) REVERT: A 640 TYR cc_start: 0.8000 (OUTLIER) cc_final: 0.7336 (t80) REVERT: H 21 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7137 (tp) REVERT: L 48 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7123 (mt) REVERT: L 67 ARG cc_start: 0.6432 (OUTLIER) cc_final: 0.5794 (ppt170) outliers start: 35 outliers final: 13 residues processed: 121 average time/residue: 0.7995 time to fit residues: 104.6365 Evaluate side-chains 108 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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 411 SER Chi-restraints excluded: chain A residue 448 VAL 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 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 98 THR Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 6 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.165321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.139498 restraints weight = 23924.983| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.25 r_work: 0.3527 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 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 = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5969 Z= 0.125 Angle : 0.620 9.168 8097 Z= 0.299 Chirality : 0.042 0.216 925 Planarity : 0.004 0.045 969 Dihedral : 6.965 68.589 1007 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.83 % Allowed : 24.60 % 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 (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: 0.87 (0.32), residues: 716 helix: 1.80 (0.28), residues: 346 sheet: 0.19 (0.53), residues: 107 loop : -0.90 (0.39), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.002 0.001 HIS A 169 PHE 0.011 0.001 PHE A 175 TYR 0.020 0.001 TYR A 590 ARG 0.002 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.00053 ( 1) link_NAG-ASN : angle 4.15066 ( 3) hydrogen bonds : bond 0.04210 ( 327) hydrogen bonds : angle 4.57201 ( 946) SS BOND : bond 0.00301 ( 8) SS BOND : angle 0.78349 ( 16) covalent geometry : bond 0.00270 ( 5960) covalent geometry : angle 0.61476 ( 8078) *********************** 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 123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.639 Fit side-chains REVERT: A 239 TYR cc_start: 0.6996 (m-10) cc_final: 0.6098 (m-10) REVERT: A 446 ASN cc_start: 0.6380 (m-40) cc_final: 0.6167 (m-40) REVERT: A 640 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7384 (t80) REVERT: H 21 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7028 (tp) REVERT: L 48 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7129 (mt) REVERT: L 67 ARG cc_start: 0.6315 (OUTLIER) cc_final: 0.5805 (ppt170) outliers start: 24 outliers final: 14 residues processed: 112 average time/residue: 0.7278 time to fit residues: 87.8628 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER 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 640 TYR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 67 ARG Chi-restraints excluded: chain L residue 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: 2.9990 chunk 22 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 1 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.165161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.139367 restraints weight = 15669.433| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.42 r_work: 0.3537 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5969 Z= 0.129 Angle : 0.636 8.501 8097 Z= 0.313 Chirality : 0.043 0.218 925 Planarity : 0.004 0.045 969 Dihedral : 6.846 58.480 1007 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.47 % Allowed : 24.44 % Favored : 71.09 % 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: 0.83 (0.32), residues: 716 helix: 1.77 (0.28), residues: 346 sheet: 0.27 (0.52), residues: 107 loop : -0.99 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 50 HIS 0.004 0.001 HIS A 520 PHE 0.011 0.001 PHE A 175 TYR 0.019 0.001 TYR A 590 ARG 0.003 0.000 ARG L 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00023 ( 1) link_NAG-ASN : angle 4.74104 ( 3) hydrogen bonds : bond 0.04279 ( 327) hydrogen bonds : angle 4.53317 ( 946) SS BOND : bond 0.00390 ( 8) SS BOND : angle 1.89995 ( 16) covalent geometry : bond 0.00283 ( 5960) covalent geometry : angle 0.62494 ( 8078) *********************** 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 127 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.612 Fit side-chains REVERT: A 446 ASN cc_start: 0.6523 (m-40) cc_final: 0.6247 (m110) REVERT: A 640 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7364 (t80) REVERT: H 21 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7017 (tp) REVERT: L 48 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7188 (mt) REVERT: L 67 ARG cc_start: 0.6380 (OUTLIER) cc_final: 0.5812 (ppt170) outliers start: 28 outliers final: 15 residues processed: 116 average time/residue: 0.8568 time to fit residues: 106.1416 Evaluate side-chains 113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 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 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 Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 10.0000 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 80 ASN ** H 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.166029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140731 restraints weight = 23034.494| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.21 r_work: 0.3538 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3535 r_free = 0.3535 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2089 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= 0.124 Angle : 0.630 8.198 8097 Z= 0.306 Chirality : 0.042 0.218 925 Planarity : 0.004 0.046 969 Dihedral : 6.440 58.716 1007 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.79 % Allowed : 25.56 % Favored : 69.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.32), residues: 716 helix: 1.82 (0.28), residues: 346 sheet: 0.28 (0.52), residues: 107 loop : -0.99 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.020 0.001 TYR A 590 ARG 0.005 0.000 ARG A 526 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 1) link_NAG-ASN : angle 5.38445 ( 3) hydrogen bonds : bond 0.04145 ( 327) hydrogen bonds : angle 4.46669 ( 946) SS BOND : bond 0.00366 ( 8) SS BOND : angle 1.46855 ( 16) covalent geometry : bond 0.00272 ( 5960) covalent geometry : angle 0.61853 ( 8078) *********************** 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 129 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 99 time to evaluate : 0.716 Fit side-chains REVERT: A 446 ASN cc_start: 0.6415 (m-40) cc_final: 0.6156 (m110) REVERT: A 640 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7309 (t80) REVERT: H 21 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6957 (tp) REVERT: L 48 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7159 (mt) REVERT: L 67 ARG cc_start: 0.6293 (OUTLIER) cc_final: 0.5700 (ppt170) outliers start: 30 outliers final: 15 residues processed: 117 average time/residue: 0.8519 time to fit residues: 107.6826 Evaluate side-chains 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 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 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 Chi-restraints excluded: chain L residue 104 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 9 optimal weight: 0.0000 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- 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 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 = 0.3997 r_free = 0.3997 target = 0.167502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.141409 restraints weight = 21910.011| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.90 r_work: 0.3581 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3580 r_free = 0.3580 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5969 Z= 0.119 Angle : 0.615 7.810 8097 Z= 0.301 Chirality : 0.042 0.217 925 Planarity : 0.004 0.045 969 Dihedral : 6.106 59.514 1007 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.99 % Allowed : 26.20 % Favored : 69.81 % 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: 1.85 (0.28), residues: 346 sheet: 0.46 (0.53), residues: 102 loop : -0.99 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.021 0.001 TYR A 590 ARG 0.004 0.000 ARG A 580 Details of bonding type rmsd link_NAG-ASN : bond 0.00017 ( 1) link_NAG-ASN : angle 5.33920 ( 3) hydrogen bonds : bond 0.04006 ( 327) hydrogen bonds : angle 4.36971 ( 946) SS BOND : bond 0.00369 ( 8) SS BOND : angle 1.28975 ( 16) covalent geometry : bond 0.00255 ( 5960) covalent geometry : angle 0.60457 ( 8078) *********************** 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 122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.598 Fit side-chains REVERT: A 83 PHE cc_start: 0.6845 (m-10) cc_final: 0.6471 (m-80) REVERT: A 180 LEU cc_start: 0.7406 (OUTLIER) cc_final: 0.6797 (mm) REVERT: A 640 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.7309 (t80) REVERT: H 21 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6907 (tp) REVERT: L 48 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7162 (mt) REVERT: L 67 ARG cc_start: 0.6257 (OUTLIER) cc_final: 0.5677 (ppt170) outliers start: 25 outliers final: 15 residues processed: 111 average time/residue: 0.7676 time to fit residues: 91.4356 Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 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 51 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 129 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 19 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 15 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.0670 chunk 55 optimal weight: 6.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140771 restraints weight = 21516.357| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.83 r_work: 0.3580 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5969 Z= 0.121 Angle : 0.612 7.707 8097 Z= 0.300 Chirality : 0.042 0.218 925 Planarity : 0.004 0.045 969 Dihedral : 5.923 59.053 1007 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 5.11 % Allowed : 24.76 % Favored : 70.13 % 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 (0.32), residues: 716 helix: 1.81 (0.28), residues: 347 sheet: 0.43 (0.53), residues: 102 loop : -0.96 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 50 HIS 0.002 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.020 0.001 TYR A 590 ARG 0.004 0.000 ARG A 580 Details of bonding type rmsd link_NAG-ASN : bond 0.00041 ( 1) link_NAG-ASN : angle 4.75555 ( 3) hydrogen bonds : bond 0.04040 ( 327) hydrogen bonds : angle 4.36834 ( 946) SS BOND : bond 0.00359 ( 8) SS BOND : angle 1.28557 ( 16) covalent geometry : bond 0.00261 ( 5960) covalent geometry : angle 0.60361 ( 8078) *********************** 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 132 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6864 (m-10) cc_final: 0.6546 (m-80) REVERT: A 180 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.6835 (mm) REVERT: A 640 TYR cc_start: 0.7892 (OUTLIER) cc_final: 0.7263 (t80) REVERT: A 650 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7912 (mptm) REVERT: H 21 LEU cc_start: 0.7264 (OUTLIER) cc_final: 0.6915 (tp) REVERT: L 48 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7165 (mt) REVERT: L 67 ARG cc_start: 0.6262 (OUTLIER) cc_final: 0.5654 (ppt170) outliers start: 32 outliers final: 20 residues processed: 120 average time/residue: 0.8151 time to fit residues: 104.4324 Evaluate side-chains 120 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 648 LYS 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 129 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 0 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 7 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.166549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140576 restraints weight = 25567.700| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 3.84 r_work: 0.3535 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5969 Z= 0.124 Angle : 0.619 7.883 8097 Z= 0.305 Chirality : 0.042 0.218 925 Planarity : 0.004 0.045 969 Dihedral : 5.848 58.654 1007 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.47 % Allowed : 26.04 % 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: 0.88 (0.32), residues: 716 helix: 1.80 (0.28), residues: 347 sheet: 0.43 (0.53), residues: 102 loop : -0.98 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS A 169 PHE 0.012 0.001 PHE A 175 TYR 0.019 0.001 TYR A 590 ARG 0.009 0.001 ARG H 70 Details of bonding type rmsd link_NAG-ASN : bond 0.00035 ( 1) link_NAG-ASN : angle 4.28844 ( 3) hydrogen bonds : bond 0.04111 ( 327) hydrogen bonds : angle 4.39630 ( 946) SS BOND : bond 0.00366 ( 8) SS BOND : angle 1.04225 ( 16) covalent geometry : bond 0.00271 ( 5960) covalent geometry : angle 0.61234 ( 8078) *********************** 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 127 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6805 (m-10) cc_final: 0.6512 (m-80) REVERT: A 180 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6867 (mm) REVERT: A 596 ASP cc_start: 0.7722 (m-30) cc_final: 0.7485 (m-30) REVERT: A 640 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.7294 (t80) REVERT: A 650 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7948 (mptm) REVERT: H 21 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6880 (tp) REVERT: L 48 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7194 (mt) outliers start: 28 outliers final: 20 residues processed: 117 average time/residue: 0.8279 time to fit residues: 103.5575 Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 580 ARG Chi-restraints excluded: chain A residue 640 TYR Chi-restraints excluded: chain A residue 648 LYS 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 129 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 54 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 ** 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 = 0.3982 r_free = 0.3982 target = 0.166249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.140288 restraints weight = 21048.791| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.86 r_work: 0.3577 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5969 Z= 0.127 Angle : 0.623 7.859 8097 Z= 0.308 Chirality : 0.042 0.219 925 Planarity : 0.004 0.046 969 Dihedral : 5.850 58.073 1007 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.15 % Allowed : 27.00 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.32), residues: 716 helix: 1.77 (0.28), residues: 347 sheet: 0.45 (0.54), residues: 102 loop : -0.98 (0.38), residues: 267 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 0.012 0.001 PHE A 175 TYR 0.019 0.001 TYR A 590 ARG 0.009 0.001 ARG H 70 Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 1) link_NAG-ASN : angle 4.05367 ( 3) hydrogen bonds : bond 0.04174 ( 327) hydrogen bonds : angle 4.41415 ( 946) SS BOND : bond 0.00375 ( 8) SS BOND : angle 1.03248 ( 16) covalent geometry : bond 0.00279 ( 5960) covalent geometry : angle 0.61726 ( 8078) ********************** 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 123 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 97 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: A 83 PHE cc_start: 0.6845 (m-10) cc_final: 0.6579 (m-80) REVERT: A 180 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.6827 (mm) REVERT: A 640 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7274 (t80) REVERT: H 21 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6895 (tp) REVERT: L 48 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7187 (mt) outliers start: 26 outliers final: 20 residues processed: 114 average time/residue: 0.7394 time to fit residues: 90.7065 Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 330 LYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 411 SER Chi-restraints excluded: chain A residue 448 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain A residue 548 SER Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 580 ARG 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 119 LEU Chi-restraints excluded: chain H residue 129 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 58 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 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 ** 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 = 0.3972 r_free = 0.3972 target = 0.164996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.139082 restraints weight = 20962.316| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.92 r_work: 0.3566 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5969 Z= 0.129 Angle : 0.623 8.015 8097 Z= 0.308 Chirality : 0.042 0.219 925 Planarity : 0.004 0.046 969 Dihedral : 5.836 57.372 1007 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 4.47 % Allowed : 26.36 % Favored : 69.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.14 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.32), residues: 716 helix: 1.72 (0.28), residues: 347 sheet: 0.46 (0.54), residues: 102 loop : -1.00 (0.38), residues: 267 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 0.018 0.001 TYR A 590 ARG 0.010 0.001 ARG H 70 Details of bonding type rmsd link_NAG-ASN : bond 0.00035 ( 1) link_NAG-ASN : angle 3.72288 ( 3) hydrogen bonds : bond 0.04213 ( 327) hydrogen bonds : angle 4.43750 ( 946) SS BOND : bond 0.00402 ( 8) SS BOND : angle 1.00335 ( 16) covalent geometry : bond 0.00284 ( 5960) covalent geometry : angle 0.61808 ( 8078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4930.89 seconds wall clock time: 87 minutes 17.98 seconds (5237.98 seconds total)