Starting phenix.real_space_refine on Thu Jul 2 09:21:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vl5_65155/07_2026/9vl5_65155.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vl5_65155/07_2026/9vl5_65155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vl5_65155/07_2026/9vl5_65155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vl5_65155/07_2026/9vl5_65155.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vl5_65155/07_2026/9vl5_65155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vl5_65155/07_2026/9vl5_65155.map" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 2 5.49 5 S 52 5.16 5 C 5074 2.51 5 N 1294 2.21 5 O 1410 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7832 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3883 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 21, 'TRANS': 498} Chain breaks: 3 Chain: "A" Number of atoms: 3939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 3939 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 21, 'TRANS': 505} Chain breaks: 2 Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.95, per 1000 atoms: 0.25 Number of scatterers: 7832 At special positions: 0 Unit cell: (89.06, 63.51, 129.94, 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 52 16.00 P 2 15.00 O 1410 8.00 N 1294 7.00 C 5074 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: 0.65 Conformation dependent library (CDL) restraints added in 595.5 milliseconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 74.5% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'B' and resid 108 through 137 removed outlier: 3.663A pdb=" N SER B 114 " --> pdb=" O ARG B 110 " (cutoff:3.500A) Proline residue: B 128 - end of helix removed outlier: 3.668A pdb=" N ILE B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 147 removed outlier: 4.206A pdb=" N GLY B 144 " --> pdb=" O PRO B 140 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.999A pdb=" N LEU B 153 " --> pdb=" O PHE B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 184 removed outlier: 3.836A pdb=" N GLN B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 183 " --> pdb=" O MET B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 214 Processing helix chain 'B' and resid 216 through 223 Processing helix chain 'B' and resid 224 through 243 Processing helix chain 'B' and resid 276 through 298 Processing helix chain 'B' and resid 301 through 307 removed outlier: 4.112A pdb=" N SER B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 323 Processing helix chain 'B' and resid 352 through 382 Processing helix chain 'B' and resid 387 through 404 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 428 through 444 removed outlier: 3.602A pdb=" N ILE B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 Processing helix chain 'B' and resid 453 through 469 removed outlier: 3.739A pdb=" N LEU B 457 " --> pdb=" O PRO B 453 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 481 removed outlier: 3.579A pdb=" N TRP B 478 " --> pdb=" O ALA B 474 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS B 479 " --> pdb=" O ALA B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 498 Processing helix chain 'B' and resid 499 through 521 Processing helix chain 'B' and resid 561 through 583 removed outlier: 4.820A pdb=" N MET B 566 " --> pdb=" O PHE B 562 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N TYR B 567 " --> pdb=" O ALA B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 621 Processing helix chain 'B' and resid 632 through 642 Processing helix chain 'B' and resid 642 through 648 removed outlier: 3.562A pdb=" N LYS B 646 " --> pdb=" O SER B 642 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 647 " --> pdb=" O VAL B 643 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE B 648 " --> pdb=" O VAL B 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 642 through 648' Processing helix chain 'B' and resid 656 through 663 Processing helix chain 'A' and resid 109 through 137 removed outlier: 3.634A pdb=" N SER A 114 " --> pdb=" O ARG A 110 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 140 through 147 removed outlier: 4.015A pdb=" N GLY A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 145 " --> pdb=" O PRO A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 159 removed outlier: 4.043A pdb=" N LEU A 153 " --> pdb=" O PHE A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 184 removed outlier: 3.767A pdb=" N GLN A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA A 183 " --> pdb=" O MET A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 214 Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 224 through 245 Processing helix chain 'A' and resid 274 through 298 Processing helix chain 'A' and resid 301 through 307 removed outlier: 4.329A pdb=" N SER A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 324 Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.601A pdb=" N LEU A 346 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 383 Processing helix chain 'A' and resid 387 through 405 removed outlier: 3.673A pdb=" N CYS A 404 " --> pdb=" O MET A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 428 through 444 removed outlier: 3.864A pdb=" N ILE A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 Processing helix chain 'A' and resid 453 through 469 removed outlier: 4.050A pdb=" N LEU A 457 " --> pdb=" O PRO A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 481 removed outlier: 3.968A pdb=" N ALA A 474 " --> pdb=" O ASP A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 498 Processing helix chain 'A' and resid 499 through 521 removed outlier: 3.711A pdb=" N ILE A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 583 removed outlier: 3.685A pdb=" N GLY A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 601 No H-bonds generated for 'chain 'A' and resid 599 through 601' Processing helix chain 'A' and resid 605 through 622 removed outlier: 3.554A pdb=" N LYS A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 622 " --> pdb=" O VAL A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 641 Processing helix chain 'A' and resid 642 through 649 Processing helix chain 'A' and resid 656 through 664 Processing sheet with id=AA1, first strand: chain 'B' and resid 166 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 536 through 538 removed outlier: 4.469A pdb=" N VAL B 553 " --> pdb=" O LYS B 527 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N PHE B 654 " --> pdb=" O LEU B 626 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU B 628 " --> pdb=" O PHE B 654 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 167 Processing sheet with id=AA4, first strand: chain 'A' and resid 536 through 538 removed outlier: 4.548A pdb=" N ASN A 523 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N VAL A 553 " --> pdb=" O LYS A 527 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N VAL A 529 " --> pdb=" O PHE A 551 " (cutoff:3.500A) removed outlier: 12.699A pdb=" N PHE A 551 " --> pdb=" O VAL A 529 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 556 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N PHE A 654 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU A 628 " --> pdb=" O PHE A 654 " (cutoff:3.500A) 579 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.08 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1952 1.33 - 1.45: 1359 1.45 - 1.57: 4562 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 7965 Sorted by residual: bond pdb=" CA PRO A 151 " pdb=" C PRO A 151 " ideal model delta sigma weight residual 1.517 1.543 -0.026 9.30e-03 1.16e+04 8.03e+00 bond pdb=" N LEU B 157 " pdb=" CA LEU B 157 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.31e-02 5.83e+03 4.64e+00 bond pdb=" SD MET B 524 " pdb=" CE MET B 524 " ideal model delta sigma weight residual 1.791 1.741 0.050 2.50e-02 1.60e+03 4.06e+00 bond pdb=" C LEU A 483 " pdb=" O LEU A 483 " ideal model delta sigma weight residual 1.237 1.214 0.022 1.19e-02 7.06e+03 3.48e+00 bond pdb=" CA VAL B 525 " pdb=" C VAL B 525 " ideal model delta sigma weight residual 1.526 1.500 0.026 1.43e-02 4.89e+03 3.38e+00 ... (remaining 7960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 10346 1.69 - 3.39: 392 3.39 - 5.08: 68 5.08 - 6.77: 9 6.77 - 8.47: 4 Bond angle restraints: 10819 Sorted by residual: angle pdb=" N VAL B 330 " pdb=" CA VAL B 330 " pdb=" C VAL B 330 " ideal model delta sigma weight residual 108.80 114.64 -5.84 1.46e+00 4.69e-01 1.60e+01 angle pdb=" C ILE A 510 " pdb=" CA ILE A 510 " pdb=" CB ILE A 510 " ideal model delta sigma weight residual 111.97 107.15 4.82 1.28e+00 6.10e-01 1.42e+01 angle pdb=" N VAL B 322 " pdb=" CA VAL B 322 " pdb=" C VAL B 322 " ideal model delta sigma weight residual 110.42 107.00 3.42 9.40e-01 1.13e+00 1.32e+01 angle pdb=" C ILE B 432 " pdb=" CA ILE B 432 " pdb=" CB ILE B 432 " ideal model delta sigma weight residual 112.14 107.26 4.88 1.35e+00 5.49e-01 1.31e+01 angle pdb=" N ARG B 622 " pdb=" CA ARG B 622 " pdb=" C ARG B 622 " ideal model delta sigma weight residual 113.02 107.70 5.32 1.49e+00 4.50e-01 1.27e+01 ... (remaining 10814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 4424 16.46 - 32.92: 283 32.92 - 49.37: 49 49.37 - 65.83: 7 65.83 - 82.29: 4 Dihedral angle restraints: 4767 sinusoidal: 1763 harmonic: 3004 Sorted by residual: dihedral pdb=" CA ASN B 358 " pdb=" CB ASN B 358 " pdb=" CG ASN B 358 " pdb=" OD1 ASN B 358 " ideal model delta sinusoidal sigma weight residual -90.00 -164.82 74.82 2 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N ALA A 126 " pdb=" CA ALA A 126 " ideal model delta harmonic sigma weight residual -180.00 -163.44 -16.56 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA VAL B 548 " pdb=" C VAL B 548 " pdb=" N PRO B 549 " pdb=" CA PRO B 549 " ideal model delta harmonic sigma weight residual -180.00 -163.91 -16.09 0 5.00e+00 4.00e-02 1.04e+01 ... (remaining 4764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 902 0.041 - 0.082: 335 0.082 - 0.123: 75 0.123 - 0.164: 24 0.164 - 0.204: 1 Chirality restraints: 1337 Sorted by residual: chirality pdb=" CA ILE A 510 " pdb=" N ILE A 510 " pdb=" C ILE A 510 " pdb=" CB ILE A 510 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CA ILE A 594 " pdb=" N ILE A 594 " pdb=" C ILE A 594 " pdb=" CB ILE A 594 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA VAL A 556 " pdb=" N VAL A 556 " pdb=" C VAL A 556 " pdb=" CB VAL A 556 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 1334 not shown) Planarity restraints: 1336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 428 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.63e+00 pdb=" C ALA B 428 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA B 428 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 429 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 328 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.26e+00 pdb=" C ILE A 328 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE A 328 " 0.012 2.00e-02 2.50e+03 pdb=" N SER A 329 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 439 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.14e+00 pdb=" C LEU B 439 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU B 439 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL B 440 " -0.010 2.00e-02 2.50e+03 ... (remaining 1333 not shown) Histogram of nonbonded interaction distances: 2.52 - 2.99: 4337 2.99 - 3.47: 8519 3.47 - 3.95: 13239 3.95 - 4.42: 15568 4.42 - 4.90: 24380 Nonbonded interactions: 66043 Sorted by model distance: nonbonded pdb=" O VAL B 644 " pdb=" OG1 THR B 647 " model vdw 2.516 3.040 nonbonded pdb=" N ARG B 622 " pdb=" N ASN B 623 " model vdw 2.564 2.560 nonbonded pdb=" OG SER B 413 " pdb=" O2 PO4 B 701 " model vdw 2.567 3.040 nonbonded pdb=" O SER A 342 " pdb=" OG SER A 342 " model vdw 2.572 3.040 nonbonded pdb=" OG SER B 499 " pdb=" OE1 GLN B 501 " model vdw 2.578 3.040 ... (remaining 66038 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 108 through 243 or resid 275 through 324 or resid 328 thro \ ugh 665 or resid 701)) selection = (chain 'B' and (resid 108 through 583 or resid 589 through 701)) } 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: 5.470 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.960 Find NCS groups from input model: 0.120 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:6.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 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 : 0.005 0.050 7965 Z= 0.259 Angle : 0.780 8.467 10819 Z= 0.448 Chirality : 0.046 0.204 1337 Planarity : 0.005 0.042 1336 Dihedral : 11.422 82.291 2831 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.12 % Allowed : 0.82 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.25), residues: 1033 helix: 0.85 (0.19), residues: 724 sheet: -0.94 (0.69), residues: 42 loop : -1.43 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 297 TYR 0.017 0.002 TYR A 408 PHE 0.020 0.002 PHE A 284 TRP 0.013 0.001 TRP A 273 HIS 0.010 0.002 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.26 ( 7965) covalent geometry : angle 0.77994 / 0.45 (10819) hydrogen bonds : bond 0.11755 / 7.95 ( 579) hydrogen bonds : angle 5.60382 / 4.15 ( 1683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 0.236 Fit side-chains REVERT: B 162 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7387 (mtt90) REVERT: B 390 LYS cc_start: 0.7367 (mttt) cc_final: 0.7147 (mtpm) REVERT: B 506 ILE cc_start: 0.7547 (mt) cc_final: 0.7327 (mm) REVERT: B 592 ARG cc_start: 0.7443 (mtp-110) cc_final: 0.6637 (ptm-80) REVERT: B 623 ASN cc_start: 0.8001 (m-40) cc_final: 0.7666 (t0) REVERT: A 191 ILE cc_start: 0.7848 (mt) cc_final: 0.7487 (mp) REVERT: A 225 LYS cc_start: 0.7272 (mttt) cc_final: 0.6831 (mmpt) REVERT: A 242 GLN cc_start: 0.6562 (mm110) cc_final: 0.5768 (mt0) REVERT: A 390 LYS cc_start: 0.7404 (mttt) cc_final: 0.6976 (mtpt) REVERT: A 489 MET cc_start: 0.6597 (mmt) cc_final: 0.6287 (mmp) REVERT: A 573 MET cc_start: 0.7780 (mmp) cc_final: 0.7520 (mmt) REVERT: A 592 ARG cc_start: 0.7514 (mtt180) cc_final: 0.6969 (mtp85) REVERT: A 637 GLU cc_start: 0.6636 (tt0) cc_final: 0.6168 (pt0) outliers start: 1 outliers final: 2 residues processed: 152 average time/residue: 0.5686 time to fit residues: 91.0975 Evaluate side-chains 113 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain A residue 344 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.147261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121667 restraints weight = 8841.095| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.07 r_work: 0.3359 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7965 Z= 0.144 Angle : 0.534 6.780 10819 Z= 0.276 Chirality : 0.040 0.141 1337 Planarity : 0.004 0.039 1336 Dihedral : 4.012 18.603 1117 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.70 % Allowed : 6.92 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1033 helix: 1.68 (0.19), residues: 727 sheet: -0.60 (0.71), residues: 42 loop : -1.25 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 622 TYR 0.017 0.001 TYR B 155 PHE 0.015 0.001 PHE A 378 TRP 0.011 0.001 TRP A 275 HIS 0.002 0.001 HIS A 293 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 7965) covalent geometry : angle 0.53376 / 0.28 (10819) hydrogen bonds : bond 0.04129 / 2.78 ( 579) hydrogen bonds : angle 4.05647 / 2.99 ( 1683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 118 time to evaluate : 0.232 Fit side-chains REVERT: B 162 ARG cc_start: 0.7929 (mtt90) cc_final: 0.6954 (mtt90) REVERT: B 390 LYS cc_start: 0.6833 (mttt) cc_final: 0.6501 (mtpm) REVERT: B 436 SER cc_start: 0.7598 (m) cc_final: 0.7086 (p) REVERT: B 506 ILE cc_start: 0.7122 (mt) cc_final: 0.6876 (mm) REVERT: B 524 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7834 (mtt) REVERT: B 573 MET cc_start: 0.7984 (mmm) cc_final: 0.7686 (mmt) REVERT: B 592 ARG cc_start: 0.7386 (mtp-110) cc_final: 0.6366 (ptm-80) REVERT: B 614 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6498 (tm-30) REVERT: B 623 ASN cc_start: 0.7875 (m-40) cc_final: 0.7385 (t0) REVERT: A 129 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: A 191 ILE cc_start: 0.7655 (mt) cc_final: 0.7281 (mp) REVERT: A 225 LYS cc_start: 0.7059 (mttt) cc_final: 0.6605 (mmpt) REVERT: A 242 GLN cc_start: 0.6576 (mm110) cc_final: 0.5817 (pt0) REVERT: A 243 GLN cc_start: 0.5005 (mm-40) cc_final: 0.4800 (tm-30) REVERT: A 390 LYS cc_start: 0.7101 (mttt) cc_final: 0.6670 (mtpt) REVERT: A 489 MET cc_start: 0.6455 (mmt) cc_final: 0.6085 (mmp) REVERT: A 557 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7419 (mt-10) REVERT: A 592 ARG cc_start: 0.7242 (mtt180) cc_final: 0.6111 (tpt170) REVERT: A 637 GLU cc_start: 0.6267 (tt0) cc_final: 0.5784 (pt0) outliers start: 23 outliers final: 7 residues processed: 128 average time/residue: 0.5003 time to fit residues: 68.0428 Evaluate side-chains 126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 620 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN B 450 HIS B 641 ASN A 138 ASN A 188 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119315 restraints weight = 8828.004| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.07 r_work: 0.3331 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7965 Z= 0.153 Angle : 0.518 6.185 10819 Z= 0.268 Chirality : 0.040 0.141 1337 Planarity : 0.004 0.040 1336 Dihedral : 3.950 17.897 1114 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.58 % Allowed : 10.33 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1033 helix: 1.83 (0.19), residues: 729 sheet: -0.42 (0.69), residues: 48 loop : -1.11 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 622 TYR 0.016 0.002 TYR B 155 PHE 0.017 0.001 PHE A 378 TRP 0.011 0.001 TRP A 275 HIS 0.002 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 ( 7965) covalent geometry : angle 0.51766 / 0.27 (10819) hydrogen bonds : bond 0.04165 / 2.79 ( 579) hydrogen bonds : angle 3.89236 / 2.86 ( 1683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.250 Fit side-chains REVERT: B 162 ARG cc_start: 0.7856 (mtt90) cc_final: 0.7443 (mtt90) REVERT: B 390 LYS cc_start: 0.6934 (mttt) cc_final: 0.6598 (mtpm) REVERT: B 414 PHE cc_start: 0.6879 (t80) cc_final: 0.6559 (t80) REVERT: B 489 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6275 (mmm) REVERT: B 506 ILE cc_start: 0.7139 (mt) cc_final: 0.6895 (mm) REVERT: B 524 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7894 (mtt) REVERT: B 543 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7645 (mmm160) REVERT: B 573 MET cc_start: 0.8027 (mmm) cc_final: 0.7743 (mmt) REVERT: B 592 ARG cc_start: 0.7360 (mtp-110) cc_final: 0.6001 (mmp-170) REVERT: B 614 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6486 (tm-30) REVERT: B 623 ASN cc_start: 0.7928 (m-40) cc_final: 0.7180 (t0) REVERT: A 129 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: A 191 ILE cc_start: 0.7665 (mt) cc_final: 0.7281 (mp) REVERT: A 225 LYS cc_start: 0.7099 (mttt) cc_final: 0.6614 (mmtt) REVERT: A 242 GLN cc_start: 0.6601 (mm110) cc_final: 0.5835 (pt0) REVERT: A 385 GLN cc_start: 0.7240 (OUTLIER) cc_final: 0.6456 (tm-30) REVERT: A 390 LYS cc_start: 0.7045 (mttt) cc_final: 0.6637 (mtpt) REVERT: A 489 MET cc_start: 0.6432 (mmt) cc_final: 0.6066 (mmp) REVERT: A 502 MET cc_start: 0.7184 (mmt) cc_final: 0.6904 (tpp) REVERT: A 557 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7371 (mt-10) REVERT: A 592 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6209 (tpt170) REVERT: A 637 GLU cc_start: 0.6257 (tt0) cc_final: 0.5826 (pt0) outliers start: 22 outliers final: 8 residues processed: 130 average time/residue: 0.4870 time to fit residues: 67.2413 Evaluate side-chains 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 557 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN B 641 ASN A 242 GLN A 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.145063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118977 restraints weight = 8989.518| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.08 r_work: 0.3310 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7965 Z= 0.148 Angle : 0.508 6.013 10819 Z= 0.263 Chirality : 0.040 0.149 1337 Planarity : 0.004 0.042 1336 Dihedral : 3.923 17.906 1114 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.70 % Allowed : 11.50 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.26), residues: 1033 helix: 1.95 (0.19), residues: 729 sheet: -0.44 (0.71), residues: 49 loop : -1.09 (0.36), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 622 TYR 0.014 0.001 TYR B 155 PHE 0.016 0.001 PHE A 378 TRP 0.009 0.001 TRP A 275 HIS 0.002 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 ( 7965) covalent geometry : angle 0.50807 / 0.26 (10819) hydrogen bonds : bond 0.04000 / 2.69 ( 579) hydrogen bonds : angle 3.80065 / 2.79 ( 1683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.231 Fit side-chains REVERT: B 162 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7001 (mtt90) REVERT: B 164 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7600 (tt) REVERT: B 390 LYS cc_start: 0.7021 (mttt) cc_final: 0.6705 (mtpm) REVERT: B 414 PHE cc_start: 0.6980 (t80) cc_final: 0.6654 (t80) REVERT: B 489 MET cc_start: 0.6615 (OUTLIER) cc_final: 0.6371 (mmm) REVERT: B 506 ILE cc_start: 0.7208 (mt) cc_final: 0.6955 (mm) REVERT: B 524 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7929 (mtt) REVERT: B 543 ARG cc_start: 0.7964 (mmm160) cc_final: 0.7685 (mmm160) REVERT: B 573 MET cc_start: 0.8136 (mmm) cc_final: 0.7875 (mmt) REVERT: B 592 ARG cc_start: 0.7430 (mtp-110) cc_final: 0.6097 (mmp-170) REVERT: B 614 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6563 (tm-30) REVERT: B 623 ASN cc_start: 0.8046 (m-40) cc_final: 0.7300 (t0) REVERT: A 129 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.6689 (mp10) REVERT: A 191 ILE cc_start: 0.7736 (mt) cc_final: 0.7350 (mp) REVERT: A 225 LYS cc_start: 0.7198 (mttt) cc_final: 0.6715 (mmtt) REVERT: A 242 GLN cc_start: 0.6812 (mm-40) cc_final: 0.6050 (pt0) REVERT: A 243 GLN cc_start: 0.5723 (tm-30) cc_final: 0.5196 (mm-40) REVERT: A 385 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: A 390 LYS cc_start: 0.7144 (mttt) cc_final: 0.6729 (mtpt) REVERT: A 489 MET cc_start: 0.6495 (mmt) cc_final: 0.6107 (mmp) REVERT: A 502 MET cc_start: 0.7253 (mmt) cc_final: 0.6965 (tpp) REVERT: A 557 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7398 (mt-10) REVERT: A 592 ARG cc_start: 0.7292 (mtt180) cc_final: 0.6281 (tpt170) REVERT: A 637 GLU cc_start: 0.6372 (tt0) cc_final: 0.5933 (pt0) outliers start: 23 outliers final: 9 residues processed: 128 average time/residue: 0.5042 time to fit residues: 68.4570 Evaluate side-chains 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 557 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 0.2980 chunk 82 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN B 641 ASN A 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.145349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119313 restraints weight = 8888.000| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.06 r_work: 0.3315 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7965 Z= 0.139 Angle : 0.498 6.528 10819 Z= 0.258 Chirality : 0.039 0.153 1337 Planarity : 0.004 0.042 1336 Dihedral : 3.899 17.460 1114 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.29 % Allowed : 12.09 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.77 (0.26), residues: 1033 helix: 2.02 (0.19), residues: 731 sheet: -0.40 (0.71), residues: 49 loop : -1.01 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 622 TYR 0.013 0.001 TYR B 155 PHE 0.015 0.001 PHE A 378 TRP 0.009 0.001 TRP A 275 HIS 0.002 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 7965) covalent geometry : angle 0.49801 / 0.26 (10819) hydrogen bonds : bond 0.03912 / 2.63 ( 579) hydrogen bonds : angle 3.75532 / 2.77 ( 1683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.217 Fit side-chains REVERT: B 162 ARG cc_start: 0.7816 (mtt90) cc_final: 0.7011 (mtt90) REVERT: B 390 LYS cc_start: 0.6947 (mttt) cc_final: 0.6627 (mtpm) REVERT: B 414 PHE cc_start: 0.6936 (t80) cc_final: 0.6607 (t80) REVERT: B 489 MET cc_start: 0.6534 (OUTLIER) cc_final: 0.6290 (mmm) REVERT: B 506 ILE cc_start: 0.7159 (mt) cc_final: 0.6908 (mm) REVERT: B 524 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7917 (mtt) REVERT: B 543 ARG cc_start: 0.7990 (mmm160) cc_final: 0.7718 (mmm160) REVERT: B 592 ARG cc_start: 0.7381 (mtp-110) cc_final: 0.6091 (mmp-170) REVERT: B 614 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6501 (tm-30) REVERT: B 623 ASN cc_start: 0.8042 (m-40) cc_final: 0.7288 (t0) REVERT: A 129 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6599 (mp10) REVERT: A 191 ILE cc_start: 0.7689 (mt) cc_final: 0.7301 (mp) REVERT: A 225 LYS cc_start: 0.7147 (mttt) cc_final: 0.6666 (mmtt) REVERT: A 242 GLN cc_start: 0.6762 (mm-40) cc_final: 0.6081 (pt0) REVERT: A 385 GLN cc_start: 0.7257 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: A 390 LYS cc_start: 0.7053 (mttt) cc_final: 0.6642 (mtpt) REVERT: A 489 MET cc_start: 0.6421 (mmt) cc_final: 0.6019 (mmp) REVERT: A 502 MET cc_start: 0.7203 (mmt) cc_final: 0.6931 (tpp) REVERT: A 557 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7357 (mt-10) REVERT: A 592 ARG cc_start: 0.7242 (mtt180) cc_final: 0.6252 (tpt170) REVERT: A 637 GLU cc_start: 0.6322 (tt0) cc_final: 0.6086 (pt0) outliers start: 28 outliers final: 10 residues processed: 129 average time/residue: 0.5264 time to fit residues: 71.9113 Evaluate side-chains 125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 489 MET Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 557 GLU Chi-restraints excluded: chain A residue 620 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN B 641 ASN A 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118524 restraints weight = 8845.417| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.06 r_work: 0.3318 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7965 Z= 0.157 Angle : 0.516 6.691 10819 Z= 0.266 Chirality : 0.040 0.163 1337 Planarity : 0.004 0.043 1336 Dihedral : 3.976 18.520 1114 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.17 % Allowed : 12.68 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.26), residues: 1033 helix: 1.97 (0.19), residues: 729 sheet: -0.37 (0.71), residues: 49 loop : -0.89 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 622 TYR 0.013 0.001 TYR B 155 PHE 0.017 0.001 PHE A 378 TRP 0.009 0.001 TRP A 275 HIS 0.002 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 7965) covalent geometry : angle 0.51580 / 0.27 (10819) hydrogen bonds : bond 0.04048 / 2.71 ( 579) hydrogen bonds : angle 3.78668 / 2.79 ( 1683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.306 Fit side-chains REVERT: B 162 ARG cc_start: 0.7826 (mtt90) cc_final: 0.7014 (mtt90) REVERT: B 164 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7604 (tt) REVERT: B 179 MET cc_start: 0.7777 (mmt) cc_final: 0.7558 (mmm) REVERT: B 390 LYS cc_start: 0.6949 (mttt) cc_final: 0.6703 (mtpm) REVERT: B 414 PHE cc_start: 0.7131 (t80) cc_final: 0.6799 (t80) REVERT: B 506 ILE cc_start: 0.7225 (mt) cc_final: 0.6971 (mm) REVERT: B 524 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7981 (mtt) REVERT: B 543 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7794 (mmm160) REVERT: B 592 ARG cc_start: 0.7398 (mtp-110) cc_final: 0.6132 (mmp-170) REVERT: B 598 MET cc_start: 0.7549 (OUTLIER) cc_final: 0.7125 (mtm) REVERT: B 614 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6566 (tm-30) REVERT: B 623 ASN cc_start: 0.8042 (m-40) cc_final: 0.7286 (t0) REVERT: A 129 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.6680 (mp10) REVERT: A 191 ILE cc_start: 0.7734 (mt) cc_final: 0.7341 (mp) REVERT: A 225 LYS cc_start: 0.7205 (mttt) cc_final: 0.6735 (mmtt) REVERT: A 242 GLN cc_start: 0.6826 (mm-40) cc_final: 0.6118 (pt0) REVERT: A 385 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.6490 (tm-30) REVERT: A 390 LYS cc_start: 0.7096 (mttt) cc_final: 0.6691 (mtpt) REVERT: A 489 MET cc_start: 0.6469 (mmt) cc_final: 0.6063 (mmp) REVERT: A 502 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6988 (tpp) REVERT: A 557 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.7344 (mt-10) REVERT: A 592 ARG cc_start: 0.7280 (mtt180) cc_final: 0.6310 (tpt170) REVERT: A 637 GLU cc_start: 0.6372 (tt0) cc_final: 0.6133 (pt0) outliers start: 27 outliers final: 10 residues processed: 125 average time/residue: 0.5276 time to fit residues: 70.1182 Evaluate side-chains 127 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 109 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 614 GLU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 344 ASN Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 557 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 72 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.6980 chunk 95 optimal weight: 0.5980 chunk 99 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 45 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 82 optimal weight: 0.0870 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN B 641 ASN A 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121407 restraints weight = 8922.369| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.05 r_work: 0.3353 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7965 Z= 0.111 Angle : 0.475 6.180 10819 Z= 0.246 Chirality : 0.038 0.166 1337 Planarity : 0.004 0.042 1336 Dihedral : 3.772 15.692 1114 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.93 % Allowed : 13.15 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.26), residues: 1033 helix: 2.23 (0.19), residues: 733 sheet: -0.21 (0.72), residues: 49 loop : -0.75 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 622 TYR 0.011 0.001 TYR B 408 PHE 0.011 0.001 PHE A 378 TRP 0.009 0.001 TRP A 275 HIS 0.001 0.000 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7965) covalent geometry : angle 0.47526 / 0.25 (10819) hydrogen bonds : bond 0.03545 / 2.36 ( 579) hydrogen bonds : angle 3.62111 / 2.67 ( 1683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.302 Fit side-chains REVERT: B 162 ARG cc_start: 0.7824 (mtt90) cc_final: 0.7137 (mtt90) REVERT: B 164 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7708 (tt) REVERT: B 390 LYS cc_start: 0.6947 (mttt) cc_final: 0.6707 (mtpm) REVERT: B 506 ILE cc_start: 0.7163 (mt) cc_final: 0.6903 (mm) REVERT: B 524 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8033 (mtt) REVERT: B 543 ARG cc_start: 0.8020 (mmm160) cc_final: 0.7732 (mmm160) REVERT: B 592 ARG cc_start: 0.7413 (mtp-110) cc_final: 0.6161 (mmp-170) REVERT: B 623 ASN cc_start: 0.8050 (m-40) cc_final: 0.7370 (t0) REVERT: A 129 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: A 191 ILE cc_start: 0.7747 (mt) cc_final: 0.7354 (mp) REVERT: A 225 LYS cc_start: 0.7216 (mttt) cc_final: 0.6752 (mmtt) REVERT: A 242 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6168 (pt0) REVERT: A 243 GLN cc_start: 0.5541 (tm-30) cc_final: 0.5041 (mm-40) REVERT: A 390 LYS cc_start: 0.7102 (mttt) cc_final: 0.6707 (mtpt) REVERT: A 489 MET cc_start: 0.6519 (mmt) cc_final: 0.6143 (mmp) REVERT: A 502 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6931 (tpp) REVERT: A 581 GLU cc_start: 0.6194 (mt-10) cc_final: 0.5964 (tm-30) REVERT: A 592 ARG cc_start: 0.7240 (mtt180) cc_final: 0.6343 (tpt170) REVERT: A 637 GLU cc_start: 0.6415 (tt0) cc_final: 0.6205 (pt0) outliers start: 25 outliers final: 12 residues processed: 127 average time/residue: 0.5493 time to fit residues: 74.0423 Evaluate side-chains 132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 358 ASN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 620 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 94 optimal weight: 0.4980 chunk 93 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN B 641 ASN A 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.146121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120856 restraints weight = 8935.692| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.02 r_work: 0.3356 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7965 Z= 0.125 Angle : 0.490 6.706 10819 Z= 0.253 Chirality : 0.039 0.167 1337 Planarity : 0.004 0.043 1336 Dihedral : 3.776 16.751 1114 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.58 % Allowed : 13.85 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.26), residues: 1033 helix: 2.25 (0.19), residues: 733 sheet: -0.15 (0.71), residues: 49 loop : -0.73 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 622 TYR 0.012 0.001 TYR B 155 PHE 0.014 0.001 PHE A 378 TRP 0.009 0.001 TRP A 275 HIS 0.002 0.000 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7965) covalent geometry : angle 0.48960 / 0.25 (10819) hydrogen bonds : bond 0.03689 / 2.46 ( 579) hydrogen bonds : angle 3.62428 / 2.68 ( 1683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.287 Fit side-chains REVERT: B 162 ARG cc_start: 0.7828 (mtt90) cc_final: 0.7552 (mtt90) REVERT: B 164 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7763 (tt) REVERT: B 390 LYS cc_start: 0.7013 (mttt) cc_final: 0.6768 (mtpm) REVERT: B 506 ILE cc_start: 0.7217 (mt) cc_final: 0.6953 (mm) REVERT: B 543 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7802 (mmm160) REVERT: B 592 ARG cc_start: 0.7444 (mtp-110) cc_final: 0.6185 (mmp-170) REVERT: B 623 ASN cc_start: 0.8075 (m-40) cc_final: 0.7417 (t0) REVERT: A 129 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: A 191 ILE cc_start: 0.7812 (mt) cc_final: 0.7419 (mp) REVERT: A 225 LYS cc_start: 0.7238 (mttt) cc_final: 0.6778 (mmtt) REVERT: A 242 GLN cc_start: 0.6848 (mm-40) cc_final: 0.6214 (pt0) REVERT: A 385 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.6533 (tm-30) REVERT: A 390 LYS cc_start: 0.7143 (mttt) cc_final: 0.6749 (mtpt) REVERT: A 489 MET cc_start: 0.6574 (mmt) cc_final: 0.6197 (mmp) REVERT: A 502 MET cc_start: 0.7247 (OUTLIER) cc_final: 0.6957 (tpp) REVERT: A 581 GLU cc_start: 0.6212 (mt-10) cc_final: 0.5978 (tm-30) REVERT: A 592 ARG cc_start: 0.7278 (mtt180) cc_final: 0.6418 (tpt170) REVERT: A 637 GLU cc_start: 0.6457 (tt0) cc_final: 0.6246 (pt0) outliers start: 22 outliers final: 11 residues processed: 129 average time/residue: 0.5202 time to fit residues: 71.2818 Evaluate side-chains 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 620 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 82 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN B 641 ASN A 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119157 restraints weight = 8924.872| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.04 r_work: 0.3341 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7965 Z= 0.146 Angle : 0.512 7.164 10819 Z= 0.264 Chirality : 0.040 0.180 1337 Planarity : 0.004 0.043 1336 Dihedral : 3.859 17.303 1114 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.58 % Allowed : 14.32 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.26), residues: 1033 helix: 2.20 (0.19), residues: 727 sheet: -0.17 (0.72), residues: 49 loop : -0.69 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 622 TYR 0.012 0.001 TYR B 155 PHE 0.016 0.001 PHE A 378 TRP 0.008 0.001 TRP A 275 HIS 0.002 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7965) covalent geometry : angle 0.51173 / 0.26 (10819) hydrogen bonds : bond 0.03881 / 2.59 ( 579) hydrogen bonds : angle 3.68869 / 2.73 ( 1683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.260 Fit side-chains REVERT: B 162 ARG cc_start: 0.7789 (mtt90) cc_final: 0.7495 (mtt90) REVERT: B 164 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7721 (tt) REVERT: B 390 LYS cc_start: 0.6952 (mttt) cc_final: 0.6709 (mtpm) REVERT: B 506 ILE cc_start: 0.7181 (mt) cc_final: 0.6927 (mm) REVERT: B 543 ARG cc_start: 0.8048 (mmm160) cc_final: 0.7816 (mmm160) REVERT: B 592 ARG cc_start: 0.7402 (mtp-110) cc_final: 0.6153 (mmp-170) REVERT: B 623 ASN cc_start: 0.7981 (m-40) cc_final: 0.7335 (t0) REVERT: A 129 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.6668 (mp10) REVERT: A 191 ILE cc_start: 0.7747 (mt) cc_final: 0.7353 (mp) REVERT: A 225 LYS cc_start: 0.7207 (mttt) cc_final: 0.6735 (mmtt) REVERT: A 242 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6193 (pt0) REVERT: A 243 GLN cc_start: 0.5508 (tm-30) cc_final: 0.4982 (mm-40) REVERT: A 385 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: A 390 LYS cc_start: 0.7120 (mttt) cc_final: 0.6717 (mtpt) REVERT: A 489 MET cc_start: 0.6518 (mmt) cc_final: 0.6146 (mmp) REVERT: A 502 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6927 (tpp) REVERT: A 557 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: A 592 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6374 (tpt170) REVERT: A 637 GLU cc_start: 0.6428 (tt0) cc_final: 0.6211 (pt0) outliers start: 22 outliers final: 10 residues processed: 123 average time/residue: 0.5127 time to fit residues: 67.0136 Evaluate side-chains 123 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN B 641 ASN A 188 GLN A 358 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119304 restraints weight = 8943.093| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.04 r_work: 0.3345 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7965 Z= 0.144 Angle : 0.513 7.093 10819 Z= 0.265 Chirality : 0.040 0.178 1337 Planarity : 0.004 0.043 1336 Dihedral : 3.880 17.864 1114 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.00 % Allowed : 14.79 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.26), residues: 1033 helix: 2.16 (0.19), residues: 727 sheet: -0.21 (0.71), residues: 49 loop : -0.72 (0.38), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 622 TYR 0.013 0.001 TYR B 155 PHE 0.016 0.001 PHE A 378 TRP 0.008 0.001 TRP A 275 HIS 0.002 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 7965) covalent geometry : angle 0.51264 / 0.26 (10819) hydrogen bonds : bond 0.03868 / 2.58 ( 579) hydrogen bonds : angle 3.71132 / 2.76 ( 1683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.313 Fit side-chains REVERT: B 162 ARG cc_start: 0.7786 (mtt90) cc_final: 0.7474 (mtt90) REVERT: B 164 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7777 (tt) REVERT: B 390 LYS cc_start: 0.6944 (mttt) cc_final: 0.6697 (mtpm) REVERT: B 506 ILE cc_start: 0.7193 (mt) cc_final: 0.6937 (mm) REVERT: B 543 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7828 (mmm160) REVERT: B 592 ARG cc_start: 0.7388 (mtp-110) cc_final: 0.6129 (mmp-170) REVERT: B 623 ASN cc_start: 0.7888 (m-40) cc_final: 0.7312 (t0) REVERT: A 129 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.6655 (mp10) REVERT: A 191 ILE cc_start: 0.7769 (mt) cc_final: 0.7376 (mp) REVERT: A 225 LYS cc_start: 0.7212 (mttt) cc_final: 0.6747 (mmtt) REVERT: A 242 GLN cc_start: 0.6832 (mm-40) cc_final: 0.6228 (pt0) REVERT: A 293 HIS cc_start: 0.7749 (t-90) cc_final: 0.7450 (t70) REVERT: A 385 GLN cc_start: 0.7250 (OUTLIER) cc_final: 0.6447 (tm-30) REVERT: A 390 LYS cc_start: 0.7162 (mttt) cc_final: 0.6755 (mtpt) REVERT: A 489 MET cc_start: 0.6522 (mmt) cc_final: 0.6154 (mmp) REVERT: A 502 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6956 (tpp) REVERT: A 557 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.7259 (mt-10) REVERT: A 592 ARG cc_start: 0.7232 (mtt180) cc_final: 0.6363 (tpt170) REVERT: A 637 GLU cc_start: 0.6457 (tt0) cc_final: 0.6225 (pt0) outliers start: 17 outliers final: 11 residues processed: 121 average time/residue: 0.5409 time to fit residues: 69.4910 Evaluate side-chains 125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 358 ASN Chi-restraints excluded: chain B residue 481 ASP Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 385 GLN Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 502 MET Chi-restraints excluded: chain A residue 556 VAL Chi-restraints excluded: chain A residue 557 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 76 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 358 ASN B 641 ASN A 358 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119588 restraints weight = 8893.313| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.03 r_work: 0.3346 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7965 Z= 0.133 Angle : 0.506 7.141 10819 Z= 0.261 Chirality : 0.039 0.176 1337 Planarity : 0.004 0.043 1336 Dihedral : 3.862 17.327 1114 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.00 % Allowed : 15.14 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.26), residues: 1033 helix: 2.20 (0.19), residues: 727 sheet: -0.22 (0.72), residues: 49 loop : -0.72 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 622 TYR 0.012 0.001 TYR B 155 PHE 0.015 0.001 PHE A 378 TRP 0.008 0.001 TRP A 275 HIS 0.002 0.001 HIS A 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 7965) covalent geometry : angle 0.50588 / 0.26 (10819) hydrogen bonds : bond 0.03791 / 2.52 ( 579) hydrogen bonds : angle 3.68523 / 2.74 ( 1683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2796.26 seconds wall clock time: 48 minutes 22.06 seconds (2902.06 seconds total)