Starting phenix.real_space_refine on Thu Jul 2 01:45:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mw7_48691/07_2026/9mw7_48691.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mw7_48691/07_2026/9mw7_48691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mw7_48691/07_2026/9mw7_48691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mw7_48691/07_2026/9mw7_48691.map" model { file = "/net/cci-nas-00/data/ceres_data/9mw7_48691/07_2026/9mw7_48691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mw7_48691/07_2026/9mw7_48691.cif" } resolution = 3.4 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= 0.010 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 P 54 5.49 5 S 23 5.16 5 C 3269 2.51 5 N 963 2.21 5 O 1191 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s 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: 5504 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 566 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 14} Link IDs: {'rna2p': 1, 'rna3p': 25} Chain: "C" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 573 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 15, 'rna3p_pyr': 12} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 4334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4334 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 25, 'TRANS': 509} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.17, per 1000 atoms: 0.21 Number of scatterers: 5504 At special positions: 0 Unit cell: (74.12, 88.944, 106.384, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 23 16.00 P 54 15.00 Al 1 13.00 F 3 9.00 O 1191 8.00 N 963 7.00 C 3269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 155.7 milliseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1030 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 4 sheets defined 44.9% alpha, 9.5% beta 23 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.694A pdb=" N VAL A 16 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 17 " --> pdb=" O PRO A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 48 removed outlier: 4.318A pdb=" N VAL A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET A 43 " --> pdb=" O PHE A 39 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.660A pdb=" N ILE A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 84 removed outlier: 3.960A pdb=" N VAL A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ASN A 74 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN A 75 " --> pdb=" O PRO A 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 83 " --> pdb=" O VAL A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 removed outlier: 3.517A pdb=" N MET A 95 " --> pdb=" O VAL A 92 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 97 " --> pdb=" O ASP A 94 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ASP A 98 " --> pdb=" O MET A 95 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N SER A 99 " --> pdb=" O GLY A 96 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP A 100 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 112 Processing helix chain 'A' and resid 118 through 128 removed outlier: 3.725A pdb=" N PHE A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.746A pdb=" N HIS A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 345 through 361 Processing helix chain 'A' and resid 362 through 365 Processing helix chain 'A' and resid 376 through 393 Processing helix chain 'A' and resid 424 through 436 Processing helix chain 'A' and resid 468 through 475 removed outlier: 3.529A pdb=" N TYR A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.687A pdb=" N ASP A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 545 removed outlier: 3.916A pdb=" N ASP A 544 " --> pdb=" O TYR A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 Processing helix chain 'A' and resid 613 through 632 removed outlier: 4.562A pdb=" N GLU A 624 " --> pdb=" O SER A 620 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N ALA A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N CYS A 626 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 631 " --> pdb=" O LYS A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 644 removed outlier: 3.742A pdb=" N LYS A 643 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 644 " --> pdb=" O PRO A 641 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 644' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 5.880A pdb=" N ILE A 28 " --> pdb=" O VAL A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 88 through 90 removed outlier: 3.869A pdb=" N VAL A 116 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR A 63 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N MET A 117 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N PHE A 65 " --> pdb=" O MET A 117 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ARG A 62 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU A 138 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 140 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG A 170 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 222 through 228 removed outlier: 4.083A pdb=" N ILE A 488 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 226 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 490 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE A 371 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP A 404 " --> pdb=" O VAL A 443 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 581 removed outlier: 3.645A pdb=" N THR A 577 " --> pdb=" O THR A 593 " (cutoff:3.500A) 146 hydrogen bonds defined for protein. 420 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 57 hydrogen bonds 114 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1536 1.34 - 1.46: 1174 1.46 - 1.57: 2864 1.57 - 1.69: 110 1.69 - 1.81: 35 Bond restraints: 5719 Sorted by residual: bond pdb=" N LYS A 149 " pdb=" CA LYS A 149 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.74e+00 bond pdb=" C4 ADP A 702 " pdb=" C5 ADP A 702 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.15e+00 bond pdb=" CB LYS A 628 " pdb=" CG LYS A 628 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.12e+00 bond pdb=" C VAL A 406 " pdb=" O VAL A 406 " ideal model delta sigma weight residual 1.245 1.231 0.014 1.41e-02 5.03e+03 9.95e-01 bond pdb=" C VAL A 448 " pdb=" O VAL A 448 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.19e-02 7.06e+03 8.05e-01 ... (remaining 5714 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 7826 1.97 - 3.95: 113 3.95 - 5.92: 21 5.92 - 7.90: 5 7.90 - 9.87: 1 Bond angle restraints: 7966 Sorted by residual: angle pdb=" O2 C C 23 " pdb=" C2 C C 23 " pdb=" N3 C C 23 " ideal model delta sigma weight residual 121.90 119.73 2.17 7.00e-01 2.04e+00 9.62e+00 angle pdb=" C1' U C 4 " pdb=" N1 U C 4 " pdb=" C2 U C 4 " ideal model delta sigma weight residual 117.70 121.22 -3.52 1.20e+00 6.94e-01 8.60e+00 angle pdb=" C PRO A 641 " pdb=" N VAL A 642 " pdb=" CA VAL A 642 " ideal model delta sigma weight residual 121.97 127.06 -5.09 1.80e+00 3.09e-01 8.00e+00 angle pdb=" CA LEU A 44 " pdb=" CB LEU A 44 " pdb=" CG LEU A 44 " ideal model delta sigma weight residual 116.30 126.17 -9.87 3.50e+00 8.16e-02 7.96e+00 angle pdb=" CA LYS A 628 " pdb=" CB LYS A 628 " pdb=" CG LYS A 628 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.52e+00 ... (remaining 7961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.29: 3035 17.29 - 34.58: 331 34.58 - 51.87: 126 51.87 - 69.16: 69 69.16 - 86.45: 17 Dihedral angle restraints: 3578 sinusoidal: 1998 harmonic: 1580 Sorted by residual: dihedral pdb=" CA ASP A 395 " pdb=" CB ASP A 395 " pdb=" CG ASP A 395 " pdb=" OD1 ASP A 395 " ideal model delta sinusoidal sigma weight residual -30.00 -89.25 59.25 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CG ARG A 547 " pdb=" CD ARG A 547 " pdb=" NE ARG A 547 " pdb=" CZ ARG A 547 " ideal model delta sinusoidal sigma weight residual 180.00 135.76 44.24 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CB GLU A 533 " pdb=" CG GLU A 533 " pdb=" CD GLU A 533 " pdb=" OE1 GLU A 533 " ideal model delta sinusoidal sigma weight residual 0.00 86.45 -86.45 1 3.00e+01 1.11e-03 1.00e+01 ... (remaining 3575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 654 0.030 - 0.060: 184 0.060 - 0.091: 48 0.091 - 0.121: 38 0.121 - 0.151: 6 Chirality restraints: 930 Sorted by residual: chirality pdb=" CG LEU A 387 " pdb=" CB LEU A 387 " pdb=" CD1 LEU A 387 " pdb=" CD2 LEU A 387 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" C1' ADP A 702 " pdb=" C2' ADP A 702 " pdb=" N9 ADP A 702 " pdb=" O4' ADP A 702 " both_signs ideal model delta sigma weight residual False 2.48 2.63 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" CA ASN A 483 " pdb=" N ASN A 483 " pdb=" C ASN A 483 " pdb=" CB ASN A 483 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 927 not shown) Planarity restraints: 821 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 220 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.91e+00 pdb=" N PRO A 221 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 221 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 221 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' C B 26 " 0.020 2.00e-02 2.50e+03 1.11e-02 2.76e+00 pdb=" N1 C B 26 " -0.026 2.00e-02 2.50e+03 pdb=" C2 C B 26 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C B 26 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C B 26 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C B 26 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C B 26 " 0.004 2.00e-02 2.50e+03 pdb=" C5 C B 26 " 0.000 2.00e-02 2.50e+03 pdb=" C6 C B 26 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 10 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 11 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 11 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 11 " -0.022 5.00e-02 4.00e+02 ... (remaining 818 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 217 2.69 - 3.24: 5539 3.24 - 3.80: 9303 3.80 - 4.35: 11697 4.35 - 4.90: 17246 Nonbonded interactions: 44002 Sorted by model distance: nonbonded pdb=" F1 AF3 A 701 " pdb=" O1B ADP A 702 " model vdw 2.138 2.990 nonbonded pdb=" O ILE A 80 " pdb=" OG1 THR A 84 " model vdw 2.179 3.040 nonbonded pdb=" O ILE A 554 " pdb=" ND1 HIS A 558 " model vdw 2.192 3.120 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 108 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR A 14 " pdb=" O SER A 35 " model vdw 2.257 3.040 ... (remaining 43997 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=1.00 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: 2.740 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.490 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6618 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 : 0.008 0.608 5721 Z= 0.815 Angle : 0.619 9.873 7966 Z= 0.360 Chirality : 0.037 0.151 930 Planarity : 0.004 0.043 821 Dihedral : 18.410 86.451 2548 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.23 % Favored : 90.58 % Rotamer: Outliers : 1.01 % Allowed : 21.50 % Favored : 77.48 % 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: -1.07 (0.37), residues: 531 helix: 0.58 (0.38), residues: 198 sheet: -0.20 (0.61), residues: 80 loop : -1.99 (0.39), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 12 TYR 0.012 0.001 TYR A 560 PHE 0.016 0.001 PHE A 39 TRP 0.002 0.001 TRP A 105 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 ( 5719) covalent geometry : angle 0.61950 / 0.36 ( 7966) hydrogen bonds : bond 0.14973 / 15.21 ( 203) hydrogen bonds : angle 5.37551 / 6.65 ( 534) Misc. bond : bond 0.42960 / 28.64 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8648 (mm) cc_final: 0.8211 (pp) REVERT: A 422 MET cc_start: 0.7759 (ppp) cc_final: 0.7218 (ppp) REVERT: A 468 ASN cc_start: 0.7961 (p0) cc_final: 0.7633 (m-40) REVERT: A 489 MET cc_start: 0.5951 (mmp) cc_final: 0.5567 (mmm) REVERT: A 550 MET cc_start: 0.7098 (ppp) cc_final: 0.6494 (ppp) REVERT: A 558 HIS cc_start: 0.8063 (m90) cc_final: 0.7603 (m90) REVERT: A 615 LYS cc_start: 0.8138 (tptt) cc_final: 0.7129 (tptp) REVERT: A 632 MET cc_start: 0.2449 (ptm) cc_final: 0.1933 (ptm) outliers start: 5 outliers final: 4 residues processed: 38 average time/residue: 0.0840 time to fit residues: 4.1452 Evaluate side-chains 38 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 554 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 54 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.2980 chunk 50 optimal weight: 0.1980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN A 113 GLN A 127 ASN A 159 HIS ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.111305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.089679 restraints weight = 28033.652| |-----------------------------------------------------------------------------| r_work (start): 0.4082 rms_B_bonded: 5.27 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.0673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5721 Z= 0.127 Angle : 0.609 8.920 7966 Z= 0.306 Chirality : 0.038 0.167 930 Planarity : 0.005 0.061 821 Dihedral : 16.637 75.645 1409 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 2.23 % Allowed : 20.08 % Favored : 77.69 % 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: -1.21 (0.37), residues: 531 helix: 0.45 (0.37), residues: 208 sheet: -0.31 (0.61), residues: 78 loop : -2.12 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.016 0.001 TYR A 560 PHE 0.012 0.001 PHE A 463 TRP 0.005 0.001 TRP A 105 HIS 0.004 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 ( 5719) covalent geometry : angle 0.60906 / 0.31 ( 7966) hydrogen bonds : bond 0.04779 / 4.76 ( 203) hydrogen bonds : angle 4.78059 / 5.96 ( 534) Misc. bond : bond 0.00481 / 0.32 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8665 (mm) cc_final: 0.8208 (pp) REVERT: A 422 MET cc_start: 0.7682 (ppp) cc_final: 0.7216 (ppp) REVERT: A 550 MET cc_start: 0.7151 (ppp) cc_final: 0.6554 (ppp) REVERT: A 558 HIS cc_start: 0.8304 (m90) cc_final: 0.7912 (m90) REVERT: A 632 MET cc_start: 0.3138 (ptm) cc_final: 0.2099 (ptm) outliers start: 11 outliers final: 4 residues processed: 42 average time/residue: 0.0594 time to fit residues: 3.4226 Evaluate side-chains 35 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 357 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 3 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.111849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.089426 restraints weight = 27627.028| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 5.27 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.0914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5721 Z= 0.113 Angle : 0.587 9.472 7966 Z= 0.291 Chirality : 0.038 0.149 930 Planarity : 0.004 0.046 821 Dihedral : 16.521 75.384 1402 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 3.45 % Allowed : 20.08 % Favored : 76.47 % 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: -1.27 (0.37), residues: 531 helix: 0.48 (0.37), residues: 207 sheet: -0.78 (0.58), residues: 85 loop : -2.08 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 21 TYR 0.015 0.001 TYR A 560 PHE 0.008 0.001 PHE A 65 TRP 0.006 0.001 TRP A 105 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 5719) covalent geometry : angle 0.58653 / 0.29 ( 7966) hydrogen bonds : bond 0.04065 / 3.94 ( 203) hydrogen bonds : angle 4.51160 / 5.69 ( 534) Misc. bond : bond 0.00300 / 0.20 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 33 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 362 ASN cc_start: 0.6686 (OUTLIER) cc_final: 0.6200 (p0) REVERT: A 422 MET cc_start: 0.7498 (ppp) cc_final: 0.7266 (ppp) REVERT: A 468 ASN cc_start: 0.7941 (p0) cc_final: 0.7625 (m-40) REVERT: A 550 MET cc_start: 0.7190 (ppp) cc_final: 0.6522 (ppp) REVERT: A 558 HIS cc_start: 0.8061 (m90) cc_final: 0.7673 (m90) REVERT: A 632 MET cc_start: 0.2844 (ptm) cc_final: 0.1457 (ptm) outliers start: 17 outliers final: 8 residues processed: 46 average time/residue: 0.0690 time to fit residues: 4.2255 Evaluate side-chains 42 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.109990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.087773 restraints weight = 27598.917| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 5.17 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5721 Z= 0.137 Angle : 0.615 10.309 7966 Z= 0.306 Chirality : 0.039 0.175 930 Planarity : 0.005 0.040 821 Dihedral : 16.522 75.691 1402 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.55 % Favored : 89.45 % Rotamer: Outliers : 2.84 % Allowed : 20.89 % Favored : 76.27 % 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: -1.36 (0.37), residues: 531 helix: 0.39 (0.36), residues: 210 sheet: -0.98 (0.56), residues: 85 loop : -2.08 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 478 TYR 0.014 0.001 TYR A 560 PHE 0.010 0.002 PHE A 463 TRP 0.005 0.001 TRP A 105 HIS 0.005 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 5719) covalent geometry : angle 0.61494 / 0.31 ( 7966) hydrogen bonds : bond 0.04352 / 4.19 ( 203) hydrogen bonds : angle 4.56622 / 5.79 ( 534) Misc. bond : bond 0.00319 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 34 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASN cc_start: 0.6733 (OUTLIER) cc_final: 0.6285 (p0) REVERT: A 468 ASN cc_start: 0.7918 (p0) cc_final: 0.7570 (m-40) REVERT: A 550 MET cc_start: 0.7180 (ppp) cc_final: 0.6679 (ppp) REVERT: A 558 HIS cc_start: 0.8094 (m90) cc_final: 0.7710 (m90) REVERT: A 615 LYS cc_start: 0.8054 (tptt) cc_final: 0.7124 (tptp) REVERT: A 632 MET cc_start: 0.2758 (ptm) cc_final: 0.1293 (ptt) outliers start: 14 outliers final: 9 residues processed: 43 average time/residue: 0.0855 time to fit residues: 4.7324 Evaluate side-chains 43 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 42 optimal weight: 0.1980 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.110188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.088034 restraints weight = 28257.994| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 5.36 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6691 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5721 Z= 0.131 Angle : 0.626 10.320 7966 Z= 0.309 Chirality : 0.039 0.161 930 Planarity : 0.004 0.038 821 Dihedral : 16.553 75.628 1402 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 2.84 % Allowed : 21.30 % Favored : 75.86 % 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: -1.47 (0.37), residues: 531 helix: 0.30 (0.36), residues: 210 sheet: -1.10 (0.56), residues: 85 loop : -2.13 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 21 TYR 0.015 0.001 TYR A 560 PHE 0.009 0.001 PHE A 65 TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 ( 5719) covalent geometry : angle 0.62558 / 0.31 ( 7966) hydrogen bonds : bond 0.04113 / 3.96 ( 203) hydrogen bonds : angle 4.53129 / 5.76 ( 534) Misc. bond : bond 0.00314 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 33 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASN cc_start: 0.6626 (OUTLIER) cc_final: 0.6202 (p0) REVERT: A 468 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7715 (m-40) REVERT: A 550 MET cc_start: 0.7174 (ppp) cc_final: 0.6645 (ppp) REVERT: A 558 HIS cc_start: 0.8248 (m90) cc_final: 0.7819 (m90) REVERT: A 615 LYS cc_start: 0.8040 (tptt) cc_final: 0.7074 (tptp) REVERT: A 632 MET cc_start: 0.2869 (ptm) cc_final: 0.1788 (ptm) outliers start: 14 outliers final: 9 residues processed: 42 average time/residue: 0.0874 time to fit residues: 4.7585 Evaluate side-chains 43 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 468 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 581 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 = 0.4464 r_free = 0.4464 target = 0.108485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.086554 restraints weight = 27888.407| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 5.06 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5721 Z= 0.171 Angle : 0.643 10.648 7966 Z= 0.321 Chirality : 0.040 0.176 930 Planarity : 0.005 0.039 821 Dihedral : 16.648 76.020 1402 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.92 % Favored : 88.89 % Rotamer: Outliers : 2.64 % Allowed : 21.91 % Favored : 75.46 % 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: -1.66 (0.36), residues: 531 helix: 0.19 (0.36), residues: 210 sheet: -1.44 (0.53), residues: 85 loop : -2.17 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 21 TYR 0.014 0.002 TYR A 560 PHE 0.013 0.002 PHE A 463 TRP 0.004 0.001 TRP A 105 HIS 0.005 0.001 HIS A 638 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 ( 5719) covalent geometry : angle 0.64260 / 0.32 ( 7966) hydrogen bonds : bond 0.04685 / 4.46 ( 203) hydrogen bonds : angle 4.60902 / 5.95 ( 534) Misc. bond : bond 0.00330 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 362 ASN cc_start: 0.6786 (OUTLIER) cc_final: 0.6369 (p0) REVERT: A 422 MET cc_start: 0.8583 (pmm) cc_final: 0.7975 (ppp) REVERT: A 550 MET cc_start: 0.7218 (ppp) cc_final: 0.6703 (ppp) REVERT: A 558 HIS cc_start: 0.8049 (m90) cc_final: 0.7674 (m90) REVERT: A 615 LYS cc_start: 0.7976 (tptt) cc_final: 0.6998 (tptp) REVERT: A 632 MET cc_start: 0.2847 (ptm) cc_final: 0.1622 (ptt) outliers start: 13 outliers final: 10 residues processed: 41 average time/residue: 0.0821 time to fit residues: 4.3287 Evaluate side-chains 44 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 117 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 468 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 40 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 21 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 ASN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.109164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.086064 restraints weight = 28098.138| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 5.69 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5721 Z= 0.132 Angle : 0.625 11.486 7966 Z= 0.309 Chirality : 0.039 0.159 930 Planarity : 0.004 0.037 821 Dihedral : 16.725 75.731 1402 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.79 % Favored : 90.02 % Rotamer: Outliers : 2.64 % Allowed : 22.52 % Favored : 74.85 % 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: -1.65 (0.36), residues: 531 helix: 0.22 (0.36), residues: 210 sheet: -1.58 (0.54), residues: 85 loop : -2.11 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 478 TYR 0.014 0.001 TYR A 560 PHE 0.010 0.001 PHE A 463 TRP 0.006 0.001 TRP A 105 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 5719) covalent geometry : angle 0.62473 / 0.31 ( 7966) hydrogen bonds : bond 0.04083 / 3.91 ( 203) hydrogen bonds : angle 4.48989 / 5.86 ( 534) Misc. bond : bond 0.00324 / 0.22 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 34 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8737 (mm) cc_final: 0.8151 (pp) REVERT: A 362 ASN cc_start: 0.7022 (OUTLIER) cc_final: 0.6594 (p0) REVERT: A 550 MET cc_start: 0.7228 (ppp) cc_final: 0.6611 (ppp) REVERT: A 558 HIS cc_start: 0.8327 (m90) cc_final: 0.7892 (m90) REVERT: A 587 ASN cc_start: 0.8040 (m-40) cc_final: 0.7796 (p0) REVERT: A 615 LYS cc_start: 0.8111 (tptt) cc_final: 0.7159 (tptp) REVERT: A 632 MET cc_start: 0.2976 (ptm) cc_final: 0.1903 (ptt) outliers start: 13 outliers final: 10 residues processed: 42 average time/residue: 0.0834 time to fit residues: 4.5102 Evaluate side-chains 44 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 33 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 458 ASN Chi-restraints excluded: chain A residue 554 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 24 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.0980 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 46 optimal weight: 0.0570 chunk 2 optimal weight: 10.0000 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 581 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 = 0.4490 r_free = 0.4490 target = 0.109869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.087197 restraints weight = 27433.628| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 5.44 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5721 Z= 0.113 Angle : 0.613 11.029 7966 Z= 0.300 Chirality : 0.038 0.149 930 Planarity : 0.004 0.036 821 Dihedral : 16.705 75.463 1402 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.98 % Favored : 89.83 % Rotamer: Outliers : 2.43 % Allowed : 22.72 % Favored : 74.85 % 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: -1.59 (0.37), residues: 531 helix: 0.33 (0.36), residues: 208 sheet: -1.57 (0.54), residues: 85 loop : -2.12 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 21 TYR 0.014 0.001 TYR A 560 PHE 0.008 0.001 PHE A 141 TRP 0.007 0.001 TRP A 105 HIS 0.003 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 5719) covalent geometry : angle 0.61326 / 0.30 ( 7966) hydrogen bonds : bond 0.03764 / 3.59 ( 203) hydrogen bonds : angle 4.35625 / 5.71 ( 534) Misc. bond : bond 0.00339 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 34 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8666 (mm) cc_final: 0.8118 (pp) REVERT: A 362 ASN cc_start: 0.6667 (OUTLIER) cc_final: 0.6320 (p0) REVERT: A 468 ASN cc_start: 0.7876 (p0) cc_final: 0.7521 (m-40) REVERT: A 550 MET cc_start: 0.7189 (ppp) cc_final: 0.6461 (ppp) REVERT: A 558 HIS cc_start: 0.8164 (m90) cc_final: 0.7682 (m90) REVERT: A 587 ASN cc_start: 0.8014 (m-40) cc_final: 0.7790 (p0) REVERT: A 615 LYS cc_start: 0.8046 (tptt) cc_final: 0.7079 (tptp) REVERT: A 632 MET cc_start: 0.2896 (ptm) cc_final: 0.1721 (ptt) outliers start: 12 outliers final: 8 residues processed: 44 average time/residue: 0.0744 time to fit residues: 4.2545 Evaluate side-chains 42 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 409 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 15 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 25 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 581 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 = 0.4501 r_free = 0.4501 target = 0.110416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.087851 restraints weight = 27438.073| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 5.32 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5721 Z= 0.116 Angle : 0.624 11.193 7966 Z= 0.304 Chirality : 0.038 0.141 930 Planarity : 0.004 0.036 821 Dihedral : 16.662 75.252 1402 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.23 % Favored : 90.58 % Rotamer: Outliers : 1.83 % Allowed : 23.12 % Favored : 75.05 % 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: -1.55 (0.36), residues: 531 helix: 0.27 (0.36), residues: 210 sheet: -1.68 (0.55), residues: 79 loop : -1.97 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 478 TYR 0.015 0.001 TYR A 560 PHE 0.008 0.001 PHE A 463 TRP 0.007 0.001 TRP A 105 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 ( 5719) covalent geometry : angle 0.62404 / 0.30 ( 7966) hydrogen bonds : bond 0.03627 / 3.41 ( 203) hydrogen bonds : angle 4.28593 / 5.64 ( 534) Misc. bond : bond 0.00312 / 0.21 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 34 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8680 (mm) cc_final: 0.8143 (pp) REVERT: A 362 ASN cc_start: 0.6726 (OUTLIER) cc_final: 0.6400 (p0) REVERT: A 468 ASN cc_start: 0.7948 (p0) cc_final: 0.7617 (m-40) REVERT: A 550 MET cc_start: 0.7154 (ppp) cc_final: 0.6407 (ppp) REVERT: A 558 HIS cc_start: 0.8084 (m90) cc_final: 0.7603 (m90) REVERT: A 587 ASN cc_start: 0.7986 (m-40) cc_final: 0.7777 (p0) REVERT: A 615 LYS cc_start: 0.8041 (tptt) cc_final: 0.7071 (tptp) REVERT: A 632 MET cc_start: 0.2847 (ptm) cc_final: 0.1652 (ptt) outliers start: 9 outliers final: 7 residues processed: 40 average time/residue: 0.0729 time to fit residues: 3.7330 Evaluate side-chains 41 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 161 LYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 409 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 8 optimal weight: 0.0770 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 54 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 overall best weight: 0.4636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.111243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.089196 restraints weight = 27686.673| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 5.21 r_work (final): 0.4063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5721 Z= 0.107 Angle : 0.609 10.955 7966 Z= 0.295 Chirality : 0.037 0.140 930 Planarity : 0.004 0.035 821 Dihedral : 16.574 74.998 1402 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.66 % Favored : 91.15 % Rotamer: Outliers : 1.42 % Allowed : 23.12 % Favored : 75.46 % 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: -1.45 (0.37), residues: 531 helix: 0.39 (0.37), residues: 210 sheet: -1.52 (0.58), residues: 79 loop : -2.00 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 478 TYR 0.016 0.001 TYR A 560 PHE 0.012 0.001 PHE A 469 TRP 0.007 0.001 TRP A 105 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 ( 5719) covalent geometry : angle 0.60929 / 0.30 ( 7966) hydrogen bonds : bond 0.03291 / 3.07 ( 203) hydrogen bonds : angle 4.09056 / 5.41 ( 534) Misc. bond : bond 0.00327 / 0.22 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 354 LEU cc_start: 0.8639 (mm) cc_final: 0.8141 (pp) REVERT: A 362 ASN cc_start: 0.6555 (OUTLIER) cc_final: 0.6331 (p0) REVERT: A 468 ASN cc_start: 0.7753 (p0) cc_final: 0.7454 (m-40) REVERT: A 550 MET cc_start: 0.7159 (ppp) cc_final: 0.6383 (ppp) REVERT: A 558 HIS cc_start: 0.7989 (m90) cc_final: 0.7477 (m90) REVERT: A 615 LYS cc_start: 0.8032 (tptt) cc_final: 0.7110 (tptp) REVERT: A 632 MET cc_start: 0.2793 (ptm) cc_final: 0.1615 (ptt) outliers start: 7 outliers final: 5 residues processed: 45 average time/residue: 0.0769 time to fit residues: 4.6192 Evaluate side-chains 40 residues out of total 493 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 362 ASN Chi-restraints excluded: chain A residue 554 ILE Chi-restraints excluded: chain A residue 581 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 57 random chunks: chunk 23 optimal weight: 0.1980 chunk 5 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.0050 chunk 50 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 overall best weight: 0.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 581 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.111451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.089118 restraints weight = 27401.345| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 5.31 r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5721 Z= 0.111 Angle : 0.619 10.833 7966 Z= 0.300 Chirality : 0.038 0.259 930 Planarity : 0.004 0.035 821 Dihedral : 16.556 74.934 1402 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.85 % Favored : 90.96 % Rotamer: Outliers : 1.01 % Allowed : 23.73 % Favored : 75.25 % 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: -1.39 (0.37), residues: 531 helix: 0.42 (0.37), residues: 210 sheet: -1.42 (0.59), residues: 79 loop : -1.98 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 21 TYR 0.016 0.001 TYR A 560 PHE 0.010 0.001 PHE A 141 TRP 0.007 0.001 TRP A 105 HIS 0.004 0.001 HIS A 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 5719) covalent geometry : angle 0.61858 / 0.30 ( 7966) hydrogen bonds : bond 0.03262 / 3.02 ( 203) hydrogen bonds : angle 4.06458 / 5.36 ( 534) Misc. bond : bond 0.00331 / 0.22 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1272.81 seconds wall clock time: 22 minutes 29.74 seconds (1349.74 seconds total)