Starting phenix.real_space_refine on Tue Jul 29 00:14:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8p0b_17332/07_2025/8p0b_17332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8p0b_17332/07_2025/8p0b_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8p0b_17332/07_2025/8p0b_17332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8p0b_17332/07_2025/8p0b_17332.map" model { file = "/net/cci-nas-00/data/ceres_data/8p0b_17332/07_2025/8p0b_17332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8p0b_17332/07_2025/8p0b_17332.cif" } resolution = 2.87 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.23, per 1000 atoms: 0.67 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: 2.84 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 3.57 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: 3.48 Time building geometry restraints manager: 3.31 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: 14795 1.32 - 2.63: 209 2.63 - 3.95: 82 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=" CA GLU A 470 " pdb=" CB GLU A 470 " pdb=" CG GLU A 470 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.20e+00 angle pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N GLY A 471 " ideal model delta sigma weight residual 114.17 117.07 -2.90 1.55e+00 4.16e-01 3.49e+00 angle pdb=" CA TYR B 533 " pdb=" CB TYR B 533 " pdb=" CG TYR B 533 " ideal model delta sigma weight residual 113.90 117.06 -3.16 1.80e+00 3.09e-01 3.09e+00 ... (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: 1091 0.028 - 0.057: 421 0.057 - 0.085: 91 0.085 - 0.114: 66 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: 5.820 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: 0.510 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 30.140 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 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= 0.131 Angle : 0.465 6.579 15096 Z= 0.238 Chirality : 0.037 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (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 TRP 0.007 0.001 TRP A 336 HIS 0.003 0.001 HIS B 475 PHE 0.008 0.001 PHE B 529 TYR 0.015 0.001 TYR B 115 ARG 0.008 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.13527 ( 480) hydrogen bonds : angle 5.21273 ( 1356) covalent geometry : bond 0.00308 (11082) covalent geometry : angle 0.46473 (15096) *********************** 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 : 1.262 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: 1.5326 time to fit residues: 213.2641 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 : 1.438 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 27 HIS B 55 GLN B 429 ASN C 131 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.062090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.041813 restraints weight = 38579.741| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 2.79 r_work: 0.2640 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11082 Z= 0.186 Angle : 0.559 7.835 15096 Z= 0.284 Chirality : 0.041 0.197 1691 Planarity : 0.005 0.077 1867 Dihedral : 10.677 116.182 1684 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.86 % Allowed : 18.01 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.24), residues: 1283 helix: 1.79 (0.22), residues: 577 sheet: -0.97 (0.39), residues: 135 loop : -0.73 (0.27), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 37 HIS 0.004 0.001 HIS B 475 PHE 0.011 0.001 PHE B 48 TYR 0.021 0.002 TYR B 533 ARG 0.009 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 480) hydrogen bonds : angle 4.36454 ( 1356) covalent geometry : bond 0.00431 (11082) covalent geometry : angle 0.55938 (15096) *********************** 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 124 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 91 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8862 (m-10) cc_final: 0.8187 (m-10) REVERT: A 87 LEU cc_start: 0.8000 (mt) cc_final: 0.7721 (mm) REVERT: B 307 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8505 (mt-10) REVERT: C 63 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8680 (mtmm) REVERT: C 80 ASN cc_start: 0.9455 (OUTLIER) cc_final: 0.9073 (t0) outliers start: 33 outliers final: 8 residues processed: 116 average time/residue: 1.4279 time to fit residues: 178.0872 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 : 1.236 ------------------------------------------------------------------------------- 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 77 LEU Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 chunk 18 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.062610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.042544 restraints weight = 39049.104| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.82 r_work: 0.2679 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11082 Z= 0.113 Angle : 0.499 5.947 15096 Z= 0.256 Chirality : 0.039 0.187 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.639 117.153 1679 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.16 % Allowed : 18.70 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.24), residues: 1283 helix: 1.87 (0.22), residues: 578 sheet: -0.89 (0.40), residues: 135 loop : -0.69 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 151 HIS 0.003 0.001 HIS B 475 PHE 0.010 0.001 PHE B 145 TYR 0.025 0.001 TYR B 104 ARG 0.008 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 480) hydrogen bonds : angle 4.17007 ( 1356) covalent geometry : bond 0.00258 (11082) covalent geometry : angle 0.49895 (15096) *********************** 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: 25 poor density : 87 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8866 (m-10) cc_final: 0.8143 (m-10) REVERT: C 63 LYS cc_start: 0.8922 (mtmm) cc_final: 0.8678 (mtmm) REVERT: C 80 ASN cc_start: 0.9473 (OUTLIER) cc_final: 0.9024 (t0) REVERT: C 86 ASP cc_start: 0.8504 (t0) cc_final: 0.7988 (t0) outliers start: 25 outliers final: 11 residues processed: 104 average time/residue: 1.5486 time to fit residues: 173.9687 Evaluate side-chains 94 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 436 VAL 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 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 77 LEU Chi-restraints excluded: chain C residue 80 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.0070 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.1980 chunk 124 optimal weight: 0.9990 overall best weight: 0.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 304 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.062493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.042425 restraints weight = 38922.294| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.83 r_work: 0.2671 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11082 Z= 0.114 Angle : 0.501 12.423 15096 Z= 0.249 Chirality : 0.039 0.201 1691 Planarity : 0.004 0.082 1867 Dihedral : 10.627 118.290 1679 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.42 % Allowed : 18.70 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.24), residues: 1283 helix: 1.91 (0.22), residues: 579 sheet: -0.88 (0.39), residues: 136 loop : -0.64 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 151 HIS 0.003 0.001 HIS B 475 PHE 0.010 0.001 PHE B 145 TYR 0.021 0.001 TYR B 533 ARG 0.012 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 480) hydrogen bonds : angle 4.02928 ( 1356) covalent geometry : bond 0.00263 (11082) covalent geometry : angle 0.50089 (15096) *********************** 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 118 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8862 (m-10) cc_final: 0.8180 (m-10) REVERT: A 48 MET cc_start: 0.6986 (mpp) cc_final: 0.6675 (pmt) REVERT: A 87 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6558 (mm) REVERT: C 63 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8696 (mtmm) REVERT: C 80 ASN cc_start: 0.9508 (OUTLIER) cc_final: 0.9046 (t0) REVERT: C 86 ASP cc_start: 0.8489 (t0) cc_final: 0.8045 (t0) outliers start: 28 outliers final: 9 residues processed: 108 average time/residue: 1.7698 time to fit residues: 207.5734 Evaluate side-chains 91 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 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 633 THR 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 114 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 18 optimal weight: 0.0170 chunk 62 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS B 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.061903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.041996 restraints weight = 38955.424| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.80 r_work: 0.2655 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.1978 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= 0.143 Angle : 0.510 9.842 15096 Z= 0.254 Chirality : 0.040 0.213 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.629 119.280 1679 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.90 % Allowed : 19.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1283 helix: 1.93 (0.22), residues: 578 sheet: -0.73 (0.39), residues: 133 loop : -0.61 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 13 HIS 0.003 0.001 HIS A 435 PHE 0.010 0.001 PHE B 145 TYR 0.021 0.001 TYR B 533 ARG 0.015 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 480) hydrogen bonds : angle 4.09217 ( 1356) covalent geometry : bond 0.00336 (11082) covalent geometry : angle 0.50961 (15096) *********************** 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 110 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8883 (m-10) cc_final: 0.8179 (m-10) REVERT: A 48 MET cc_start: 0.6934 (mpp) cc_final: 0.6680 (pmt) REVERT: A 87 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7186 (mm) REVERT: C 63 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8705 (mtmm) REVERT: C 80 ASN cc_start: 0.9518 (OUTLIER) cc_final: 0.9073 (t0) REVERT: C 86 ASP cc_start: 0.8444 (t0) cc_final: 0.8243 (p0) outliers start: 22 outliers final: 11 residues processed: 104 average time/residue: 1.7611 time to fit residues: 198.5582 Evaluate side-chains 96 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 1.453 ------------------------------------------------------------------------------- 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 153 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 88 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 126 optimal weight: 0.0570 chunk 87 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3418 r_free = 0.3418 target = 0.062136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.042295 restraints weight = 39252.645| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 2.81 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: 0.8930 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11082 Z= 0.116 Angle : 0.499 9.389 15096 Z= 0.248 Chirality : 0.040 0.226 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.615 120.814 1679 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.99 % Allowed : 20.09 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.24), residues: 1283 helix: 1.97 (0.22), residues: 578 sheet: -0.68 (0.40), residues: 127 loop : -0.61 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 13 HIS 0.003 0.000 HIS A 435 PHE 0.010 0.001 PHE B 145 TYR 0.021 0.001 TYR B 533 ARG 0.010 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03381 ( 480) hydrogen bonds : angle 4.03438 ( 1356) covalent geometry : bond 0.00271 (11082) covalent geometry : angle 0.49926 (15096) *********************** 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 108 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8863 (m-10) cc_final: 0.8150 (m-10) REVERT: C 63 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8695 (mtmm) REVERT: C 80 ASN cc_start: 0.9508 (OUTLIER) cc_final: 0.9033 (t0) outliers start: 23 outliers final: 11 residues processed: 101 average time/residue: 1.7097 time to fit residues: 187.8330 Evaluate side-chains 94 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.061075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.040980 restraints weight = 39574.742| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.82 r_work: 0.2629 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11082 Z= 0.187 Angle : 0.535 8.801 15096 Z= 0.268 Chirality : 0.041 0.221 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.656 121.909 1679 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.73 % Allowed : 20.78 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.24), residues: 1283 helix: 1.85 (0.22), residues: 578 sheet: -0.70 (0.40), residues: 127 loop : -0.64 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 13 HIS 0.003 0.001 HIS A 435 PHE 0.011 0.001 PHE B 529 TYR 0.022 0.002 TYR B 533 ARG 0.013 0.001 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03784 ( 480) hydrogen bonds : angle 4.17728 ( 1356) covalent geometry : bond 0.00438 (11082) covalent geometry : angle 0.53458 (15096) *********************** 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 101 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 TRP cc_start: 0.8862 (m-10) cc_final: 0.8185 (m-10) REVERT: C 63 LYS cc_start: 0.9123 (mtmm) cc_final: 0.8799 (mtmm) REVERT: C 80 ASN cc_start: 0.9524 (OUTLIER) cc_final: 0.9104 (t0) outliers start: 20 outliers final: 11 residues processed: 95 average time/residue: 1.4107 time to fit residues: 144.9806 Evaluate side-chains 92 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 153 VAL 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 107 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 83 optimal weight: 0.8980 chunk 53 optimal weight: 0.0060 chunk 96 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3427 r_free = 0.3427 target = 0.062430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.042676 restraints weight = 39122.083| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.79 r_work: 0.2690 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11082 Z= 0.097 Angle : 0.514 8.996 15096 Z= 0.254 Chirality : 0.039 0.274 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.625 123.628 1679 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.56 % Allowed : 20.78 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.24), residues: 1283 helix: 2.00 (0.22), residues: 579 sheet: -0.74 (0.40), residues: 127 loop : -0.61 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 13 HIS 0.002 0.000 HIS A 435 PHE 0.010 0.001 PHE B 145 TYR 0.020 0.001 TYR B 533 ARG 0.014 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03196 ( 480) hydrogen bonds : angle 4.03722 ( 1356) covalent geometry : bond 0.00220 (11082) covalent geometry : angle 0.51405 (15096) *********************** 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 102 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.5495 (pmt) cc_final: 0.4443 (pp-130) REVERT: C 63 LYS cc_start: 0.9032 (mtmm) cc_final: 0.8712 (mtmm) REVERT: C 80 ASN cc_start: 0.9475 (OUTLIER) cc_final: 0.8991 (t0) outliers start: 18 outliers final: 9 residues processed: 97 average time/residue: 2.4866 time to fit residues: 262.5387 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 : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR 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 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 45 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3410 r_free = 0.3410 target = 0.061741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.041927 restraints weight = 39791.828| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.86 r_work: 0.2664 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11082 Z= 0.130 Angle : 0.536 8.637 15096 Z= 0.266 Chirality : 0.040 0.260 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.629 123.369 1679 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.56 % Allowed : 20.95 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1283 helix: 1.96 (0.22), residues: 579 sheet: -0.74 (0.40), residues: 127 loop : -0.62 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 13 HIS 0.002 0.000 HIS A 435 PHE 0.010 0.001 PHE B 145 TYR 0.020 0.001 TYR B 533 ARG 0.015 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03395 ( 480) hydrogen bonds : angle 4.10464 ( 1356) covalent geometry : bond 0.00309 (11082) covalent geometry : angle 0.53605 (15096) *********************** 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 102 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.5502 (pmt) cc_final: 0.4442 (pp-130) REVERT: C 63 LYS cc_start: 0.9079 (mtmm) cc_final: 0.8755 (mtmm) REVERT: C 80 ASN cc_start: 0.9477 (OUTLIER) cc_final: 0.9010 (t0) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 1.4595 time to fit residues: 149.1762 Evaluate side-chains 92 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 61 LYS 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 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 76 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 109 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.061702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.041923 restraints weight = 39570.259| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.79 r_work: 0.2667 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11082 Z= 0.128 Angle : 0.525 9.358 15096 Z= 0.261 Chirality : 0.040 0.247 1691 Planarity : 0.004 0.081 1867 Dihedral : 10.612 123.248 1679 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.21 % Allowed : 21.30 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.24), residues: 1283 helix: 1.97 (0.22), residues: 579 sheet: -0.71 (0.41), residues: 127 loop : -0.64 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 13 HIS 0.002 0.000 HIS A 435 PHE 0.010 0.001 PHE B 145 TYR 0.021 0.001 TYR B 533 ARG 0.012 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 480) hydrogen bonds : angle 4.09140 ( 1356) covalent geometry : bond 0.00304 (11082) covalent geometry : angle 0.52504 (15096) ********************** 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 99 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.5661 (pmt) cc_final: 0.4542 (pp-130) REVERT: A 146 CYS cc_start: 0.9065 (m) cc_final: 0.8603 (p) REVERT: C 63 LYS cc_start: 0.9103 (mtmm) cc_final: 0.8772 (mtmm) REVERT: C 80 ASN cc_start: 0.9487 (OUTLIER) cc_final: 0.9018 (t0) REVERT: C 98 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8395 (ttm-80) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 1.3523 time to fit residues: 138.5743 Evaluate side-chains 94 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 TYR Chi-restraints excluded: chain A residue 61 LYS 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 633 THR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 80 ASN Chi-restraints excluded: chain C residue 98 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 18 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.061964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.042120 restraints weight = 39684.332| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 2.84 r_work: 0.2678 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11082 Z= 0.115 Angle : 0.536 11.725 15096 Z= 0.263 Chirality : 0.040 0.297 1691 Planarity : 0.004 0.080 1867 Dihedral : 10.600 122.336 1679 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.39 % Allowed : 21.04 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.24), residues: 1283 helix: 1.96 (0.22), residues: 579 sheet: -0.72 (0.41), residues: 127 loop : -0.64 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP A 13 HIS 0.002 0.000 HIS A 403 PHE 0.010 0.001 PHE B 145 TYR 0.020 0.001 TYR B 533 ARG 0.016 0.000 ARG A 31 Details of bonding type rmsd hydrogen bonds : bond 0.03321 ( 480) hydrogen bonds : angle 4.09249 ( 1356) covalent geometry : bond 0.00272 (11082) covalent geometry : angle 0.53635 (15096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7810.40 seconds wall clock time: 145 minutes 5.17 seconds (8705.17 seconds total)