Starting phenix.real_space_refine on Wed Aug 5 16:56:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p0b_17332/08_2026/8p0b_17332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p0b_17332/08_2026/8p0b_17332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8p0b_17332/08_2026/8p0b_17332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p0b_17332/08_2026/8p0b_17332.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8p0b_17332/08_2026/8p0b_17332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p0b_17332/08_2026/8p0b_17332.map" } resolution = 2.87 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= 0.001 sd= 0.012 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: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 63 5.16 5 C 6792 2.51 5 N 1868 2.21 5 O 2066 1.98 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10807 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 618, 4987 Classifications: {'peptide': 618} Link IDs: {'PTRANS': 31, 'TRANS': 586} Chain breaks: 1 Chain: "B" Number of atoms: 4703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4703 Classifications: {'peptide': 590} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 558} Chain breaks: 2 Chain: "C" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 730 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 6, 'TRANS': 82} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 123 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 3} Chain: "V" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Classifications: {'RNA': 12} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 7, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 8} Time building chain proxies: 2.66, per 1000 atoms: 0.25 Number of scatterers: 10807 At special positions: 0 Unit cell: (103.375, 120.742, 98.413, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 18 15.00 O 2066 8.00 N 1868 7.00 C 6792 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=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 375.1 milliseconds 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 14 sheets defined 48.1% alpha, 11.7% beta 1 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 removed outlier: 4.226A pdb=" N GLU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 25 removed outlier: 3.761A pdb=" N THR A 24 " --> pdb=" O ASP A 21 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A 25 " --> pdb=" O TRP A 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 21 through 25' Processing helix chain 'A' and resid 29 through 48 removed outlier: 4.067A pdb=" N MET A 48 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 removed outlier: 3.618A pdb=" N ILE A 68 " --> pdb=" O ASP A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 155 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 177 through 184 Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.707A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 304 through 315 Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.043A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 380 Processing helix chain 'A' and resid 382 through 400 Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 517 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 3.583A pdb=" N ARG A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.639A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 removed outlier: 3.678A pdb=" N MET A 617 " --> pdb=" O GLY A 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 5 Processing helix chain 'B' and resid 13 through 19 removed outlier: 3.926A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 49 Proline residue: B 44 - end of helix removed outlier: 4.664A pdb=" N TYR B 49 " --> pdb=" O TYR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'B' and resid 95 through 108 Processing helix chain 'B' and resid 108 through 113 removed outlier: 4.017A pdb=" N LYS B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.521A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 344 removed outlier: 3.804A pdb=" N MET B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) Proline residue: B 338 - end of helix Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.359A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 408 removed outlier: 3.592A pdb=" N SER B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 451 Processing helix chain 'B' and resid 456 through 459 Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 552 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 587 through 595 Processing helix chain 'C' and resid 51 through 62 removed outlier: 5.168A pdb=" N VAL C 58 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N TYR C 59 " --> pdb=" O MET C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 115 through 136 removed outlier: 4.994A pdb=" N ALA C 125 " --> pdb=" O ALA C 121 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLU C 126 " --> pdb=" O ILE C 122 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 101 removed outlier: 6.552A pdb=" N LEU A 99 " --> pdb=" O PHE A 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 removed outlier: 4.545A pdb=" N ASN B 453 " --> pdb=" O GLU B 303 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 237 through 238 removed outlier: 4.428A pdb=" N ILE A 450 " --> pdb=" O GLU A 238 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 423 through 431 current: chain 'A' and resid 463 through 469 removed outlier: 6.771A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 468 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU A 259 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.324A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 527 Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 177 Processing sheet with id=AB2, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.740A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS B 345 " --> pdb=" O CYS B 387 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS B 387 " --> pdb=" O LYS B 345 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB4, first strand: chain 'B' and resid 633 through 634 removed outlier: 4.781A pdb=" N THR B 633 " --> pdb=" O SER C 68 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 98 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 78 through 79 492 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3 hydrogen bonds 6 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 1.66 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3551 1.36 - 1.51: 3156 1.51 - 1.66: 4271 1.66 - 1.80: 79 1.80 - 1.95: 25 Bond restraints: 11082 Sorted by residual: bond pdb=" SD MET A 48 " pdb=" CE MET A 48 " ideal model delta sigma weight residual 1.791 1.950 -0.159 2.50e-02 1.60e+03 4.02e+01 bond pdb=" CG MET A 48 " pdb=" SD MET A 48 " ideal model delta sigma weight residual 1.803 1.952 -0.149 2.50e-02 1.60e+03 3.55e+01 bond pdb=" CB GLU A 470 " pdb=" CG GLU A 470 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.13e+00 bond pdb=" N MET B 1 " pdb=" CA MET B 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 bond pdb=" CA GLU A 470 " pdb=" CB GLU A 470 " ideal model delta sigma weight residual 1.532 1.545 -0.013 1.36e-02 5.41e+03 9.76e-01 ... (remaining 11077 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 14747 1.32 - 2.63: 256 2.63 - 3.95: 83 3.95 - 5.26: 7 5.26 - 6.58: 3 Bond angle restraints: 15096 Sorted by residual: angle pdb=" N GLU A 470 " pdb=" CA GLU A 470 " pdb=" C GLU A 470 " ideal model delta sigma weight residual 111.02 105.70 5.32 1.25e+00 6.40e-01 1.81e+01 angle pdb=" CB GLU A 470 " pdb=" CG GLU A 470 " pdb=" CD GLU A 470 " ideal model delta sigma weight residual 112.60 119.18 -6.58 1.70e+00 3.46e-01 1.50e+01 angle pdb=" O5' A V 7 " pdb=" C5' A V 7 " pdb=" C4' A V 7 " ideal model delta sigma weight residual 109.40 112.45 -3.05 8.00e-01 1.56e+00 1.45e+01 angle pdb=" O4' A V 7 " pdb=" C1' A V 7 " pdb=" N9 A V 7 " ideal model delta sigma weight residual 108.20 110.82 -2.62 8.00e-01 1.56e+00 1.07e+01 angle pdb=" O5' C R 31 " pdb=" C5' C R 31 " pdb=" C4' C R 31 " ideal model delta sigma weight residual 109.40 111.97 -2.57 8.00e-01 1.56e+00 1.03e+01 ... (remaining 15091 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.22: 6143 23.22 - 46.43: 478 46.43 - 69.65: 94 69.65 - 92.86: 17 92.86 - 116.08: 2 Dihedral angle restraints: 6734 sinusoidal: 2940 harmonic: 3794 Sorted by residual: dihedral pdb=" CG ARG B 323 " pdb=" CD ARG B 323 " pdb=" NE ARG B 323 " pdb=" CZ ARG B 323 " ideal model delta sinusoidal sigma weight residual 180.00 135.15 44.85 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CB GLU B 170 " pdb=" CG GLU B 170 " pdb=" CD GLU B 170 " pdb=" OE1 GLU B 170 " ideal model delta sinusoidal sigma weight residual 0.00 87.89 -87.89 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CG ARG B 315 " pdb=" CD ARG B 315 " pdb=" NE ARG B 315 " pdb=" CZ ARG B 315 " ideal model delta sinusoidal sigma weight residual -180.00 -136.39 -43.61 2 1.50e+01 4.44e-03 1.02e+01 ... (remaining 6731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1084 0.028 - 0.057: 408 0.057 - 0.085: 95 0.085 - 0.114: 82 0.114 - 0.142: 22 Chirality restraints: 1691 Sorted by residual: chirality pdb=" CA VAL B 275 " pdb=" N VAL B 275 " pdb=" C VAL B 275 " pdb=" CB VAL B 275 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE C 75 " pdb=" N ILE C 75 " pdb=" C ILE C 75 " pdb=" CB ILE C 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE B 212 " pdb=" N ILE B 212 " pdb=" C ILE B 212 " pdb=" CB ILE B 212 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 1688 not shown) Planarity restraints: 1867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 470 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.24e+00 pdb=" C GLU A 470 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 470 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 471 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 273 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO B 274 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 274 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 274 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 196 " -0.146 9.50e-02 1.11e+02 6.57e-02 2.83e+00 pdb=" NE ARG A 196 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 196 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 196 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 196 " -0.003 2.00e-02 2.50e+03 ... (remaining 1864 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 184 2.65 - 3.21: 10045 3.21 - 3.77: 17250 3.77 - 4.34: 24455 4.34 - 4.90: 39538 Nonbonded interactions: 91472 Sorted by model distance: nonbonded pdb=" OG SER A 466 " pdb=" OE1 GLN A 473 " model vdw 2.084 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OP1 G V 2 " model vdw 2.103 3.040 nonbonded pdb=" O GLU A 470 " pdb=" OE1 GLU A 470 " model vdw 2.108 3.040 nonbonded pdb=" O THR A 269 " pdb=" OG SER A 463 " model vdw 2.116 3.040 nonbonded pdb=" O ASP C 86 " pdb=" OG1 THR C 97 " model vdw 2.140 3.040 ... (remaining 91467 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: 7.210 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.740 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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 : 0.003 0.159 11082 Z= 0.134 Angle : 0.479 6.579 15096 Z= 0.265 Chirality : 0.039 0.142 1691 Planarity : 0.004 0.066 1867 Dihedral : 16.906 116.076 4274 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.73 % Allowed : 18.87 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1283 helix: 1.73 (0.23), residues: 578 sheet: -0.99 (0.38), residues: 143 loop : -0.88 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 196 TYR 0.015 0.001 TYR B 115 PHE 0.008 0.001 PHE B 529 TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 (11082) covalent geometry : angle 0.47861 / 0.26 (15096) hydrogen bonds : bond 0.13527 / 9.59 ( 480) hydrogen bonds : angle 5.21273 / 3.64 ( 1356) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 6 residues processed: 130 average time/residue: 0.6250 time to fit residues: 87.0245 Evaluate side-chains 91 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 ASP Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain B residue 299 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.0270 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 HIS A 27 HIS B 55 GLN B 531 HIS C 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.062334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.042010 restraints weight = 38914.852| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.83 r_work: 0.2643 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11082 Z= 0.193 Angle : 0.575 9.021 15096 Z= 0.293 Chirality : 0.042 0.203 1691 Planarity : 0.005 0.074 1867 Dihedral : 10.657 112.345 1684 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.68 % Allowed : 18.79 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1283 helix: 1.70 (0.22), residues: 578 sheet: -1.02 (0.39), residues: 135 loop : -0.77 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 196 TYR 0.023 0.002 TYR B 533 PHE 0.016 0.001 PHE B 48 TRP 0.013 0.001 TRP A 37 HIS 0.004 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.19 (11082) covalent geometry : angle 0.57518 / 0.29 (15096) hydrogen bonds : bond 0.04556 / 3.11 ( 480) hydrogen bonds : angle 4.46386 / 3.13 ( 1356) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 LEU cc_start: 0.7944 (mt) cc_final: 0.7680 (mm) REVERT: B 307 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.8519 (mt-10) REVERT: C 63 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8662 (mtmm) outliers start: 31 outliers final: 9 residues processed: 114 average time/residue: 0.5394 time to fit residues: 66.2404 Evaluate side-chains 91 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 77 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 22 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 93 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 12 optimal weight: 0.0050 chunk 70 optimal weight: 0.0020 overall best weight: 0.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 HIS B 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.062352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.042190 restraints weight = 38782.226| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.82 r_work: 0.2659 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11082 Z= 0.136 Angle : 0.522 6.173 15096 Z= 0.267 Chirality : 0.040 0.202 1691 Planarity : 0.005 0.079 1867 Dihedral : 10.632 111.991 1679 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.25 % Allowed : 18.70 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1283 helix: 1.80 (0.22), residues: 577 sheet: -0.96 (0.39), residues: 135 loop : -0.73 (0.26), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 98 TYR 0.022 0.001 TYR B 533 PHE 0.009 0.001 PHE B 145 TRP 0.028 0.001 TRP A 13 HIS 0.003 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (11082) covalent geometry : angle 0.52200 / 0.27 (15096) hydrogen bonds : bond 0.03997 / 2.72 ( 480) hydrogen bonds : angle 4.27442 / 3.00 ( 1356) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8880 (m-10) cc_final: 0.8155 (m-10) REVERT: C 63 LYS cc_start: 0.8981 (mtmm) cc_final: 0.8745 (mtmm) REVERT: C 80 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9244 (t0) outliers start: 26 outliers final: 10 residues processed: 107 average time/residue: 0.5437 time to fit residues: 62.8039 Evaluate side-chains 93 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 103 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 7 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 111 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 HIS B 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.061804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.041677 restraints weight = 39385.791| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.83 r_work: 0.2640 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9118 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11082 Z= 0.163 Angle : 0.536 10.774 15096 Z= 0.269 Chirality : 0.041 0.199 1691 Planarity : 0.004 0.080 1867 Dihedral : 10.637 111.328 1679 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.34 % Allowed : 19.22 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.24), residues: 1283 helix: 1.72 (0.22), residues: 585 sheet: -0.81 (0.40), residues: 126 loop : -0.79 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 196 TYR 0.027 0.001 TYR B 104 PHE 0.010 0.001 PHE B 145 TRP 0.018 0.001 TRP A 13 HIS 0.003 0.001 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (11082) covalent geometry : angle 0.53582 / 0.27 (15096) hydrogen bonds : bond 0.03884 / 2.63 ( 480) hydrogen bonds : angle 4.21415 / 2.97 ( 1356) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8906 (m-10) cc_final: 0.8200 (m-10) REVERT: A 149 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7691 (mt) REVERT: C 63 LYS cc_start: 0.9018 (mtmm) cc_final: 0.8756 (mtmm) REVERT: C 80 ASN cc_start: 0.9502 (OUTLIER) cc_final: 0.9051 (t0) outliers start: 27 outliers final: 13 residues processed: 105 average time/residue: 0.5742 time to fit residues: 64.7165 Evaluate side-chains 94 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 11 ASN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 54 GLN Chi-restraints excluded: chain C residue 68 SER Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 chunk 90 optimal weight: 0.3980 chunk 118 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 HIS B 429 ASN B 531 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.062322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.042486 restraints weight = 38949.606| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.83 r_work: 0.2669 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9090 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11082 Z= 0.106 Angle : 0.507 10.154 15096 Z= 0.254 Chirality : 0.040 0.213 1691 Planarity : 0.004 0.082 1867 Dihedral : 10.631 111.807 1679 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.16 % Allowed : 19.39 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.24), residues: 1283 helix: 1.81 (0.22), residues: 584 sheet: -0.80 (0.40), residues: 126 loop : -0.75 (0.26), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 196 TYR 0.021 0.001 TYR B 104 PHE 0.010 0.001 PHE B 145 TRP 0.013 0.001 TRP A 13 HIS 0.003 0.001 HIS B 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (11082) covalent geometry : angle 0.50729 / 0.25 (15096) hydrogen bonds : bond 0.03533 / 2.39 ( 480) hydrogen bonds : angle 4.09284 / 2.88 ( 1356) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8877 (m-10) cc_final: 0.8162 (m-10) REVERT: C 63 LYS cc_start: 0.9011 (mtmm) cc_final: 0.8752 (mtmm) REVERT: C 80 ASN cc_start: 0.9512 (OUTLIER) cc_final: 0.9051 (t0) outliers start: 25 outliers final: 8 residues processed: 102 average time/residue: 0.5012 time to fit residues: 55.1665 Evaluate side-chains 87 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 78 optimal weight: 0.0870 chunk 103 optimal weight: 0.0870 chunk 116 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 HIS B 475 HIS B 531 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.062413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.042585 restraints weight = 39044.305| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.80 r_work: 0.2677 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9102 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11082 Z= 0.111 Angle : 0.508 9.471 15096 Z= 0.255 Chirality : 0.040 0.214 1691 Planarity : 0.004 0.082 1867 Dihedral : 10.615 112.114 1679 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.16 % Allowed : 19.65 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.24), residues: 1283 helix: 1.89 (0.22), residues: 578 sheet: -0.80 (0.39), residues: 126 loop : -0.71 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 196 TYR 0.021 0.001 TYR B 533 PHE 0.010 0.001 PHE B 145 TRP 0.012 0.001 TRP A 13 HIS 0.007 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (11082) covalent geometry : angle 0.50795 / 0.25 (15096) hydrogen bonds : bond 0.03409 / 2.31 ( 480) hydrogen bonds : angle 4.05015 / 2.86 ( 1356) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8851 (m-10) cc_final: 0.8168 (m-10) REVERT: A 149 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7610 (mt) REVERT: C 63 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8748 (mtmm) REVERT: C 80 ASN cc_start: 0.9509 (OUTLIER) cc_final: 0.9021 (t0) outliers start: 25 outliers final: 10 residues processed: 99 average time/residue: 0.5567 time to fit residues: 59.1880 Evaluate side-chains 91 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 32 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 0.0570 chunk 7 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 10 optimal weight: 0.0030 chunk 127 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 0.5108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS B 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.062655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.042702 restraints weight = 39038.948| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.87 r_work: 0.2672 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11082 Z= 0.109 Angle : 0.511 9.042 15096 Z= 0.256 Chirality : 0.040 0.247 1691 Planarity : 0.004 0.082 1867 Dihedral : 10.589 112.854 1679 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.47 % Allowed : 20.00 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.24), residues: 1283 helix: 1.88 (0.22), residues: 578 sheet: -0.78 (0.40), residues: 127 loop : -0.68 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 196 TYR 0.020 0.001 TYR B 533 PHE 0.010 0.001 PHE B 145 TRP 0.017 0.001 TRP C 65 HIS 0.002 0.001 HIS A 403 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11082) covalent geometry : angle 0.51067 / 0.26 (15096) hydrogen bonds : bond 0.03348 / 2.26 ( 480) hydrogen bonds : angle 4.05131 / 2.86 ( 1356) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8870 (m-10) cc_final: 0.8161 (m-10) REVERT: A 48 MET cc_start: 0.7030 (pmm) cc_final: 0.5740 (pp-130) REVERT: A 149 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7613 (mt) REVERT: C 63 LYS cc_start: 0.8996 (mtmm) cc_final: 0.8693 (mtmm) REVERT: C 80 ASN cc_start: 0.9515 (OUTLIER) cc_final: 0.9004 (t0) outliers start: 17 outliers final: 10 residues processed: 93 average time/residue: 0.6044 time to fit residues: 60.6599 Evaluate side-chains 93 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 120 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS B 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.062177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.042297 restraints weight = 39486.034| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.85 r_work: 0.2672 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9101 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11082 Z= 0.130 Angle : 0.519 8.707 15096 Z= 0.259 Chirality : 0.040 0.292 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.579 113.391 1679 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.65 % Allowed : 20.35 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.24), residues: 1283 helix: 1.91 (0.22), residues: 578 sheet: -0.73 (0.40), residues: 127 loop : -0.68 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 196 TYR 0.021 0.001 TYR B 533 PHE 0.010 0.001 PHE B 145 TRP 0.012 0.001 TRP C 65 HIS 0.003 0.000 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (11082) covalent geometry : angle 0.51942 / 0.26 (15096) hydrogen bonds : bond 0.03402 / 2.30 ( 480) hydrogen bonds : angle 4.05799 / 2.87 ( 1356) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8863 (m-10) cc_final: 0.8166 (m-10) REVERT: C 63 LYS cc_start: 0.9039 (mtmm) cc_final: 0.8742 (mtmm) REVERT: C 80 ASN cc_start: 0.9505 (OUTLIER) cc_final: 0.9001 (t0) outliers start: 19 outliers final: 9 residues processed: 97 average time/residue: 0.5649 time to fit residues: 59.2581 Evaluate side-chains 90 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS B 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.061986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.042042 restraints weight = 39099.974| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.85 r_work: 0.2665 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9106 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11082 Z= 0.134 Angle : 0.527 8.574 15096 Z= 0.263 Chirality : 0.040 0.254 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.569 114.071 1679 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.39 % Allowed : 20.87 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1283 helix: 1.92 (0.22), residues: 578 sheet: -0.71 (0.40), residues: 127 loop : -0.68 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 31 TYR 0.021 0.001 TYR B 533 PHE 0.010 0.001 PHE B 145 TRP 0.025 0.001 TRP A 151 HIS 0.003 0.000 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (11082) covalent geometry : angle 0.52728 / 0.26 (15096) hydrogen bonds : bond 0.03441 / 2.32 ( 480) hydrogen bonds : angle 4.06119 / 2.87 ( 1356) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8845 (m-10) cc_final: 0.8155 (m-10) REVERT: A 48 MET cc_start: 0.6838 (pmm) cc_final: 0.6546 (pmm) REVERT: C 63 LYS cc_start: 0.9064 (mtmm) cc_final: 0.8749 (mtmm) REVERT: C 80 ASN cc_start: 0.9502 (OUTLIER) cc_final: 0.8996 (t0) outliers start: 16 outliers final: 8 residues processed: 93 average time/residue: 0.6005 time to fit residues: 60.4575 Evaluate side-chains 89 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 38 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 99 optimal weight: 0.5980 chunk 117 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 110 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS B 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.062124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.042228 restraints weight = 39205.821| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.84 r_work: 0.2670 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9103 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11082 Z= 0.120 Angle : 0.536 9.226 15096 Z= 0.265 Chirality : 0.040 0.249 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.554 115.105 1679 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.30 % Allowed : 20.95 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.24), residues: 1283 helix: 1.95 (0.22), residues: 578 sheet: -0.70 (0.40), residues: 127 loop : -0.69 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 196 TYR 0.020 0.001 TYR B 533 PHE 0.010 0.001 PHE B 145 TRP 0.030 0.001 TRP A 151 HIS 0.003 0.000 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (11082) covalent geometry : angle 0.53605 / 0.27 (15096) hydrogen bonds : bond 0.03362 / 2.29 ( 480) hydrogen bonds : angle 4.03570 / 2.86 ( 1356) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2566 Ramachandran restraints generated. 1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8843 (m-10) cc_final: 0.8150 (m-10) REVERT: A 48 MET cc_start: 0.6855 (pmm) cc_final: 0.6566 (pmm) REVERT: B 314 MET cc_start: 0.9303 (mtm) cc_final: 0.9067 (mtt) REVERT: C 63 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8741 (mtmm) REVERT: C 80 ASN cc_start: 0.9502 (OUTLIER) cc_final: 0.8999 (t0) outliers start: 15 outliers final: 8 residues processed: 91 average time/residue: 0.5715 time to fit residues: 56.0452 Evaluate side-chains 90 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 475 HIS Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS B 531 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.062352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.042461 restraints weight = 39520.484| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.88 r_work: 0.2676 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9099 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11082 Z= 0.114 Angle : 0.538 9.920 15096 Z= 0.265 Chirality : 0.040 0.243 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.539 115.974 1679 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.21 % Allowed : 21.21 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1283 helix: 1.97 (0.22), residues: 578 sheet: -0.70 (0.40), residues: 127 loop : -0.68 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 196 TYR 0.020 0.001 TYR B 533 PHE 0.011 0.001 PHE B 145 TRP 0.036 0.001 TRP A 151 HIS 0.002 0.000 HIS A 435 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (11082) covalent geometry : angle 0.53779 / 0.27 (15096) hydrogen bonds : bond 0.03331 / 2.25 ( 480) hydrogen bonds : angle 4.01300 / 2.84 ( 1356) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2994.52 seconds wall clock time: 51 minutes 55.23 seconds (3115.23 seconds total)