Starting phenix.real_space_refine on Wed Sep 17 10:27:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izq_61039/09_2025/9izq_61039.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izq_61039/09_2025/9izq_61039.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9izq_61039/09_2025/9izq_61039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izq_61039/09_2025/9izq_61039.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9izq_61039/09_2025/9izq_61039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izq_61039/09_2025/9izq_61039.map" } resolution = 3.06 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 ------------------------------------------------------------------------------- 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= 0.016 sd= 0.197 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: 6 Type Number sf(0) Gaussians P 96 5.49 5 Mg 2 5.21 5 S 30 5.16 5 C 4864 2.51 5 N 1370 2.21 5 O 1799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8161 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 6140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 739, 6140 Classifications: {'peptide': 739} Link IDs: {'PTRANS': 12, 'TRANS': 726} Chain: "B" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1127 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 7, 'rna3p_pur': 24, 'rna3p_pyr': 19} Link IDs: {'rna2p': 9, 'rna3p': 43} Chain: "C" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 564 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.08, per 1000 atoms: 0.25 Number of scatterers: 8161 At special positions: 0 Unit cell: (90.885, 95.865, 109.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 30 16.00 P 96 15.00 Mg 2 11.99 O 1799 8.00 N 1370 7.00 C 4864 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: 0.94 Conformation dependent library (CDL) restraints added in 258.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 5 sheets defined 51.7% alpha, 9.2% beta 32 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 42 through 54 removed outlier: 3.601A pdb=" N MET A 46 " --> pdb=" O THR A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 63 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 85 through 99 removed outlier: 3.540A pdb=" N LYS A 98 " --> pdb=" O TYR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 119 through 134 Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 168 through 181 removed outlier: 3.714A pdb=" N TRP A 172 " --> pdb=" O LYS A 168 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 177 " --> pdb=" O ASP A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 removed outlier: 4.039A pdb=" N GLU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 218 Processing helix chain 'A' and resid 270 through 274 removed outlier: 3.512A pdb=" N ASN A 274 " --> pdb=" O ARG A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 287 removed outlier: 4.182A pdb=" N ASP A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA A 282 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 353 removed outlier: 3.657A pdb=" N LEU A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 removed outlier: 3.968A pdb=" N LEU A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 371 removed outlier: 3.603A pdb=" N LYS A 368 " --> pdb=" O ASN A 364 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.756A pdb=" N GLN A 402 " --> pdb=" O CYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 459 removed outlier: 3.955A pdb=" N VAL A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 Processing helix chain 'A' and resid 483 through 519 removed outlier: 3.618A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY A 519 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 571 removed outlier: 3.623A pdb=" N ASN A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 605 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 614 through 623 removed outlier: 3.720A pdb=" N GLU A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 693 removed outlier: 3.513A pdb=" N TYR A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 691 " --> pdb=" O ILE A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 701 removed outlier: 3.587A pdb=" N GLU A 698 " --> pdb=" O GLU A 694 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE A 699 " --> pdb=" O VAL A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 237 removed outlier: 6.892A pdb=" N ASN A 290 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER A 305 " --> pdb=" O ASN A 290 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU A 300 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 5 " --> pdb=" O PHE A 304 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU A 266 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 242 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 379 removed outlier: 5.345A pdb=" N GLU A 336 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N PHE A 379 " --> pdb=" O THR A 334 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A 334 " --> pdb=" O PHE A 379 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N GLY A 322 " --> pdb=" O SER A 335 " (cutoff:3.500A) removed outlier: 9.544A pdb=" N LYS A 337 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 12.887A pdb=" N THR A 320 " --> pdb=" O LYS A 337 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL A 321 " --> pdb=" O ALA A 524 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N GLU A 526 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N LEU A 323 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 578 removed outlier: 3.764A pdb=" N ASP A 586 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 650 through 652 Processing sheet with id=AA5, first strand: chain 'A' and resid 667 through 668 removed outlier: 3.679A pdb=" N LYS A 672 " --> pdb=" O THR A 668 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 810 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 1.54 Time building geometry restraints manager: 1.20 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: 1695 1.33 - 1.45: 2338 1.45 - 1.57: 4242 1.57 - 1.69: 190 1.69 - 1.81: 47 Bond restraints: 8512 Sorted by residual: bond pdb=" CA ASN A 184 " pdb=" CB ASN A 184 " ideal model delta sigma weight residual 1.522 1.531 -0.009 7.00e-03 2.04e+04 1.49e+00 bond pdb=" O4' DA C -1 " pdb=" C1' DA C -1 " ideal model delta sigma weight residual 1.414 1.395 0.019 2.00e-02 2.50e+03 9.33e-01 bond pdb=" CB ILE A 690 " pdb=" CG2 ILE A 690 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.87e-01 bond pdb=" C ILE A 291 " pdb=" N VAL A 292 " ideal model delta sigma weight residual 1.330 1.319 0.011 1.26e-02 6.30e+03 7.50e-01 bond pdb=" O4' DC D 19 " pdb=" C1' DC D 19 " ideal model delta sigma weight residual 1.414 1.397 0.017 2.00e-02 2.50e+03 7.13e-01 ... (remaining 8507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 11593 1.55 - 3.09: 282 3.09 - 4.64: 19 4.64 - 6.19: 1 6.19 - 7.73: 1 Bond angle restraints: 11896 Sorted by residual: angle pdb=" C2' G B 1 " pdb=" C1' G B 1 " pdb=" N9 G B 1 " ideal model delta sigma weight residual 112.00 115.66 -3.66 1.50e+00 4.44e-01 5.97e+00 angle pdb=" N GLU A 68 " pdb=" CA GLU A 68 " pdb=" C GLU A 68 " ideal model delta sigma weight residual 113.50 110.55 2.95 1.23e+00 6.61e-01 5.75e+00 angle pdb=" N GLU A 738 " pdb=" CA GLU A 738 " pdb=" C GLU A 738 " ideal model delta sigma weight residual 107.23 111.19 -3.96 1.67e+00 3.59e-01 5.63e+00 angle pdb=" C2' G B -33 " pdb=" C1' G B -33 " pdb=" N9 G B -33 " ideal model delta sigma weight residual 112.00 115.35 -3.35 1.50e+00 4.44e-01 4.97e+00 angle pdb=" CA LEU A 100 " pdb=" CB LEU A 100 " pdb=" CG LEU A 100 " ideal model delta sigma weight residual 116.30 108.57 7.73 3.50e+00 8.16e-02 4.88e+00 ... (remaining 11891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.05: 4432 20.05 - 40.10: 452 40.10 - 60.15: 210 60.15 - 80.20: 38 80.20 - 100.25: 2 Dihedral angle restraints: 5134 sinusoidal: 2924 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ARG A 420 " pdb=" C ARG A 420 " pdb=" N THR A 421 " pdb=" CA THR A 421 " ideal model delta harmonic sigma weight residual 180.00 -162.52 -17.48 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP A 67 " pdb=" CB ASP A 67 " pdb=" CG ASP A 67 " pdb=" OD1 ASP A 67 " ideal model delta sinusoidal sigma weight residual -30.00 -88.12 58.12 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CB GLU A 692 " pdb=" CG GLU A 692 " pdb=" CD GLU A 692 " pdb=" OE1 GLU A 692 " ideal model delta sinusoidal sigma weight residual 0.00 -89.70 89.70 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 5131 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 939 0.034 - 0.069: 314 0.069 - 0.103: 73 0.103 - 0.138: 21 0.138 - 0.172: 3 Chirality restraints: 1350 Sorted by residual: chirality pdb=" C1' G B 1 " pdb=" O4' G B 1 " pdb=" C2' G B 1 " pdb=" N9 G B 1 " both_signs ideal model delta sigma weight residual False 2.46 2.29 0.17 2.00e-01 2.50e+01 7.41e-01 chirality pdb=" C1' G B -33 " pdb=" O4' G B -33 " pdb=" C2' G B -33 " pdb=" N9 G B -33 " both_signs ideal model delta sigma weight residual False 2.46 2.30 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" C1' A B -6 " pdb=" O4' A B -6 " pdb=" C2' A B -6 " pdb=" N9 A B -6 " both_signs ideal model delta sigma weight residual False 2.46 2.31 0.15 2.00e-01 2.50e+01 5.27e-01 ... (remaining 1347 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 1 " -0.028 2.00e-02 2.50e+03 1.20e-02 4.35e+00 pdb=" N9 G B 1 " 0.029 2.00e-02 2.50e+03 pdb=" C8 G B 1 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B 1 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 1 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B 1 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 1 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 1 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G B 1 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 1 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G B 1 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B -33 " -0.025 2.00e-02 2.50e+03 1.09e-02 3.55e+00 pdb=" N9 G B -33 " 0.027 2.00e-02 2.50e+03 pdb=" C8 G B -33 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G B -33 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G B -33 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B -33 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B -33 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B -33 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G B -33 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B -33 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B -33 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G B -33 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 633 " -0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A 634 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 634 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 634 " -0.020 5.00e-02 4.00e+02 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 99 2.62 - 3.19: 6720 3.19 - 3.76: 13225 3.76 - 4.33: 19401 4.33 - 4.90: 28690 Nonbonded interactions: 68135 Sorted by model distance: nonbonded pdb=" OD1 ASP A 499 " pdb="MG MG A 801 " model vdw 2.052 2.170 nonbonded pdb=" OP1 G B -30 " pdb="MG MG A 801 " model vdw 2.111 2.170 nonbonded pdb=" OH TYR A 512 " pdb=" O THR A 628 " model vdw 2.149 3.040 nonbonded pdb=" OD1 ASP A 462 " pdb=" O2' C B 14 " model vdw 2.167 3.040 nonbonded pdb=" ND2 ASN A 532 " pdb=" OG SER A 635 " model vdw 2.172 3.120 ... (remaining 68130 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: 0.090 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.290 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.004 0.029 8512 Z= 0.203 Angle : 0.567 7.733 11896 Z= 0.335 Chirality : 0.038 0.172 1350 Planarity : 0.003 0.036 1166 Dihedral : 18.612 100.252 3706 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.58 % Allowed : 7.40 % Favored : 92.02 % 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 aren not related in a simple way. whole: -0.74 (0.31), residues: 737 helix: 0.14 (0.27), residues: 363 sheet: -0.32 (0.58), residues: 84 loop : -1.26 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 697 TYR 0.014 0.002 TYR A 437 PHE 0.011 0.002 PHE A 612 TRP 0.008 0.001 TRP A 696 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00439 ( 8512) covalent geometry : angle 0.56672 (11896) hydrogen bonds : bond 0.18919 ( 357) hydrogen bonds : angle 6.11187 ( 970) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 125 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9059 (ttt) cc_final: 0.8719 (ttm) REVERT: A 356 ASP cc_start: 0.7909 (t0) cc_final: 0.7503 (t0) REVERT: A 589 TYR cc_start: 0.7322 (OUTLIER) cc_final: 0.6539 (m-80) outliers start: 4 outliers final: 0 residues processed: 128 average time/residue: 0.1139 time to fit residues: 18.6833 Evaluate side-chains 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 589 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 165 ASN A 297 ASN A 506 ASN A 517 GLN A 530 ASN A 537 GLN A 599 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.177852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128913 restraints weight = 10634.061| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.06 r_work: 0.3186 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8512 Z= 0.191 Angle : 0.550 8.461 11896 Z= 0.307 Chirality : 0.038 0.158 1350 Planarity : 0.003 0.030 1166 Dihedral : 20.636 101.662 2101 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.31 % Allowed : 12.05 % Favored : 86.65 % 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 aren not related in a simple way. whole: -0.31 (0.31), residues: 737 helix: 0.64 (0.27), residues: 367 sheet: -0.29 (0.54), residues: 95 loop : -1.26 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 667 TYR 0.014 0.002 TYR A 93 PHE 0.033 0.002 PHE A 612 TRP 0.011 0.002 TRP A 696 HIS 0.002 0.001 HIS A 230 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 8512) covalent geometry : angle 0.54965 (11896) hydrogen bonds : bond 0.05146 ( 357) hydrogen bonds : angle 4.21109 ( 970) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9044 (ttt) cc_final: 0.8700 (ttm) REVERT: A 356 ASP cc_start: 0.8004 (t0) cc_final: 0.7658 (t0) REVERT: A 452 LYS cc_start: 0.8561 (ttmm) cc_final: 0.8042 (ttmm) REVERT: A 589 TYR cc_start: 0.7170 (OUTLIER) cc_final: 0.6747 (m-10) outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.0929 time to fit residues: 11.4294 Evaluate side-chains 76 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 6.9990 chunk 26 optimal weight: 0.2980 chunk 28 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 68 optimal weight: 7.9990 chunk 22 optimal weight: 0.0370 chunk 47 optimal weight: 30.0000 chunk 42 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 overall best weight: 2.3862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 ASN A 530 ASN A 537 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.178486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.129849 restraints weight = 10511.594| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.02 r_work: 0.3202 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8512 Z= 0.166 Angle : 0.512 9.045 11896 Z= 0.286 Chirality : 0.037 0.151 1350 Planarity : 0.003 0.027 1166 Dihedral : 20.524 100.632 2101 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.74 % Allowed : 12.05 % Favored : 86.21 % 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 aren not related in a simple way. whole: 0.07 (0.31), residues: 737 helix: 0.99 (0.28), residues: 362 sheet: -0.24 (0.53), residues: 95 loop : -1.04 (0.38), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 280 TYR 0.012 0.002 TYR A 93 PHE 0.021 0.002 PHE A 480 TRP 0.008 0.001 TRP A 696 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 8512) covalent geometry : angle 0.51230 (11896) hydrogen bonds : bond 0.04562 ( 357) hydrogen bonds : angle 3.92676 ( 970) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9046 (ttt) cc_final: 0.8738 (ttm) REVERT: A 356 ASP cc_start: 0.8085 (t0) cc_final: 0.7787 (t0) REVERT: A 588 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8873 (mppt) REVERT: A 650 MET cc_start: 0.6515 (ptt) cc_final: 0.6003 (mtm) REVERT: A 694 GLU cc_start: 0.8049 (mp0) cc_final: 0.7729 (mp0) outliers start: 12 outliers final: 6 residues processed: 85 average time/residue: 0.0923 time to fit residues: 10.8298 Evaluate side-chains 76 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 0 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 64 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 ASN A 537 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.174579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.124343 restraints weight = 10850.809| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.11 r_work: 0.3131 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 8512 Z= 0.266 Angle : 0.578 9.761 11896 Z= 0.318 Chirality : 0.040 0.173 1350 Planarity : 0.003 0.026 1166 Dihedral : 20.551 101.411 2099 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.74 % Allowed : 14.22 % Favored : 84.03 % 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 aren not related in a simple way. whole: -0.25 (0.31), residues: 737 helix: 0.71 (0.27), residues: 371 sheet: -0.49 (0.51), residues: 95 loop : -1.19 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 280 TYR 0.017 0.002 TYR A 93 PHE 0.026 0.002 PHE A 612 TRP 0.010 0.002 TRP A 696 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 8512) covalent geometry : angle 0.57845 (11896) hydrogen bonds : bond 0.05122 ( 357) hydrogen bonds : angle 3.95601 ( 970) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8953 (ttt) cc_final: 0.8672 (ttm) REVERT: A 356 ASP cc_start: 0.8070 (t0) cc_final: 0.7771 (t0) REVERT: A 458 MET cc_start: 0.8301 (tpt) cc_final: 0.8058 (tpp) REVERT: A 588 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8860 (mppt) REVERT: A 706 LYS cc_start: 0.7721 (ptmm) cc_final: 0.7507 (ptmm) outliers start: 12 outliers final: 10 residues processed: 84 average time/residue: 0.0918 time to fit residues: 10.7024 Evaluate side-chains 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 23 optimal weight: 4.9990 chunk 65 optimal weight: 20.0000 chunk 59 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.177237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.129421 restraints weight = 10663.402| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.99 r_work: 0.3217 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.004 0.052 8512 Z= 0.157 Angle : 0.502 9.593 11896 Z= 0.281 Chirality : 0.037 0.146 1350 Planarity : 0.003 0.024 1166 Dihedral : 20.425 100.096 2099 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.45 % Allowed : 14.80 % Favored : 83.74 % 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 aren not related in a simple way. whole: 0.22 (0.31), residues: 737 helix: 1.20 (0.28), residues: 360 sheet: -0.34 (0.52), residues: 95 loop : -1.01 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 474 TYR 0.011 0.001 TYR A 437 PHE 0.021 0.002 PHE A 612 TRP 0.008 0.001 TRP A 696 HIS 0.002 0.000 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8512) covalent geometry : angle 0.50169 (11896) hydrogen bonds : bond 0.04233 ( 357) hydrogen bonds : angle 3.75069 ( 970) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.9040 (ttt) cc_final: 0.8796 (ttm) REVERT: A 356 ASP cc_start: 0.8082 (t0) cc_final: 0.7809 (t0) REVERT: A 458 MET cc_start: 0.8316 (tpt) cc_final: 0.8073 (tpp) REVERT: A 588 LYS cc_start: 0.9038 (mmtt) cc_final: 0.8800 (mppt) REVERT: A 706 LYS cc_start: 0.7739 (ptmm) cc_final: 0.7443 (ptmm) outliers start: 10 outliers final: 8 residues processed: 80 average time/residue: 0.0981 time to fit residues: 10.9254 Evaluate side-chains 78 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 72 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.0770 chunk 39 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 overall best weight: 0.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.181120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.133231 restraints weight = 10607.676| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.02 r_work: 0.3256 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8512 Z= 0.110 Angle : 0.488 8.922 11896 Z= 0.272 Chirality : 0.035 0.158 1350 Planarity : 0.003 0.024 1166 Dihedral : 20.331 97.785 2099 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.87 % Allowed : 15.38 % Favored : 83.74 % 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 aren not related in a simple way. whole: 0.51 (0.32), residues: 737 helix: 1.43 (0.28), residues: 361 sheet: -0.17 (0.51), residues: 95 loop : -0.87 (0.39), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 474 TYR 0.012 0.001 TYR A 437 PHE 0.019 0.001 PHE A 480 TRP 0.007 0.001 TRP A 33 HIS 0.002 0.000 HIS A 673 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8512) covalent geometry : angle 0.48821 (11896) hydrogen bonds : bond 0.03659 ( 357) hydrogen bonds : angle 3.60029 ( 970) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 83 time to evaluate : 0.218 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.8999 (ttt) cc_final: 0.8653 (ttm) REVERT: A 155 MET cc_start: 0.8185 (tpp) cc_final: 0.7868 (tpt) REVERT: A 218 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7642 (mm-40) REVERT: A 474 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7424 (mtm-85) REVERT: A 588 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8813 (mppt) REVERT: A 667 ARG cc_start: 0.8221 (ttm170) cc_final: 0.7878 (tpp80) outliers start: 6 outliers final: 6 residues processed: 86 average time/residue: 0.1006 time to fit residues: 11.6888 Evaluate side-chains 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 526 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 17 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.176700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.126870 restraints weight = 10640.300| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 1.98 r_work: 0.3171 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 8512 Z= 0.247 Angle : 0.569 8.330 11896 Z= 0.312 Chirality : 0.040 0.174 1350 Planarity : 0.003 0.023 1166 Dihedral : 20.384 99.666 2099 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.31 % Allowed : 15.09 % Favored : 83.60 % 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 aren not related in a simple way. whole: 0.08 (0.31), residues: 737 helix: 1.10 (0.28), residues: 367 sheet: -0.38 (0.54), residues: 85 loop : -1.16 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 280 TYR 0.018 0.002 TYR A 93 PHE 0.022 0.002 PHE A 612 TRP 0.008 0.002 TRP A 696 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 8512) covalent geometry : angle 0.56903 (11896) hydrogen bonds : bond 0.04770 ( 357) hydrogen bonds : angle 3.73846 ( 970) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8944 (ttt) cc_final: 0.8662 (ttm) REVERT: A 218 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7615 (mm-40) REVERT: A 356 ASP cc_start: 0.8061 (t0) cc_final: 0.7780 (t0) REVERT: A 384 ASN cc_start: 0.8852 (t0) cc_final: 0.8645 (t0) REVERT: A 588 LYS cc_start: 0.9055 (mmtt) cc_final: 0.8779 (mppt) REVERT: A 621 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8674 (tt) outliers start: 9 outliers final: 8 residues processed: 82 average time/residue: 0.0904 time to fit residues: 10.0603 Evaluate side-chains 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 675 ASN Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.178862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.130049 restraints weight = 10551.008| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.98 r_work: 0.3212 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8512 Z= 0.150 Angle : 0.522 8.832 11896 Z= 0.288 Chirality : 0.037 0.154 1350 Planarity : 0.003 0.025 1166 Dihedral : 20.331 98.580 2099 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.31 % Allowed : 15.53 % Favored : 83.16 % 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 aren not related in a simple way. whole: 0.36 (0.31), residues: 737 helix: 1.38 (0.28), residues: 361 sheet: -0.33 (0.54), residues: 85 loop : -1.01 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 474 TYR 0.012 0.002 TYR A 93 PHE 0.022 0.002 PHE A 480 TRP 0.007 0.001 TRP A 696 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8512) covalent geometry : angle 0.52208 (11896) hydrogen bonds : bond 0.04040 ( 357) hydrogen bonds : angle 3.64136 ( 970) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9041 (ttt) cc_final: 0.8802 (ttm) REVERT: A 384 ASN cc_start: 0.8789 (t0) cc_final: 0.8584 (t0) REVERT: A 474 ARG cc_start: 0.7835 (mtm-85) cc_final: 0.7359 (mtm-85) REVERT: A 588 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8822 (mppt) REVERT: A 621 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8606 (tt) REVERT: A 667 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7817 (tpp80) outliers start: 9 outliers final: 8 residues processed: 80 average time/residue: 0.0856 time to fit residues: 9.5615 Evaluate side-chains 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 4 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 39 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.178857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.129976 restraints weight = 10609.428| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.02 r_work: 0.3214 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8512 Z= 0.148 Angle : 0.523 8.543 11896 Z= 0.287 Chirality : 0.037 0.151 1350 Planarity : 0.003 0.026 1166 Dihedral : 20.322 98.138 2099 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.60 % Allowed : 15.67 % Favored : 82.73 % 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 aren not related in a simple way. whole: 0.34 (0.31), residues: 737 helix: 1.37 (0.28), residues: 364 sheet: -0.36 (0.54), residues: 85 loop : -1.06 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 474 TYR 0.013 0.001 TYR A 93 PHE 0.025 0.002 PHE A 612 TRP 0.008 0.001 TRP A 696 HIS 0.002 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 8512) covalent geometry : angle 0.52344 (11896) hydrogen bonds : bond 0.03968 ( 357) hydrogen bonds : angle 3.58909 ( 970) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9020 (ttt) cc_final: 0.8786 (ttm) REVERT: A 218 GLN cc_start: 0.7954 (mm-40) cc_final: 0.7552 (mm-40) REVERT: A 384 ASN cc_start: 0.8820 (t0) cc_final: 0.8618 (t0) REVERT: A 474 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7335 (mtm-85) REVERT: A 588 LYS cc_start: 0.9103 (mmtt) cc_final: 0.8817 (mppt) REVERT: A 621 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8579 (tt) REVERT: A 637 PHE cc_start: 0.7072 (m-80) cc_final: 0.6837 (m-80) REVERT: A 667 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7810 (tpp80) REVERT: A 706 LYS cc_start: 0.7769 (ptmm) cc_final: 0.7490 (ptmm) outliers start: 11 outliers final: 9 residues processed: 81 average time/residue: 0.0860 time to fit residues: 9.6398 Evaluate side-chains 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 37 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 39 optimal weight: 10.0000 chunk 11 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 69 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 50 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 0.0970 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.180275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.131809 restraints weight = 10618.446| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.01 r_work: 0.3239 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8512 Z= 0.119 Angle : 0.519 9.324 11896 Z= 0.284 Chirality : 0.036 0.156 1350 Planarity : 0.003 0.024 1166 Dihedral : 20.334 97.565 2099 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.16 % Allowed : 16.11 % Favored : 82.73 % 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 aren not related in a simple way. whole: 0.48 (0.32), residues: 737 helix: 1.52 (0.28), residues: 364 sheet: -0.19 (0.57), residues: 78 loop : -1.07 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 474 TYR 0.012 0.001 TYR A 437 PHE 0.023 0.002 PHE A 612 TRP 0.007 0.001 TRP A 696 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 8512) covalent geometry : angle 0.51913 (11896) hydrogen bonds : bond 0.03766 ( 357) hydrogen bonds : angle 3.55358 ( 970) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9027 (ttt) cc_final: 0.8794 (ttm) REVERT: A 218 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7517 (mm-40) REVERT: A 474 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7338 (mtm-85) REVERT: A 588 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8792 (mppt) REVERT: A 621 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8584 (tt) REVERT: A 637 PHE cc_start: 0.7029 (m-80) cc_final: 0.6799 (m-80) REVERT: A 667 ARG cc_start: 0.8254 (ttm170) cc_final: 0.7796 (tpp80) outliers start: 8 outliers final: 6 residues processed: 80 average time/residue: 0.0894 time to fit residues: 9.8837 Evaluate side-chains 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 5.9990 chunk 14 optimal weight: 40.0000 chunk 7 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 46 optimal weight: 30.0000 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.177375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128309 restraints weight = 10572.124| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.99 r_work: 0.3183 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 8512 Z= 0.221 Angle : 0.571 8.739 11896 Z= 0.311 Chirality : 0.039 0.166 1350 Planarity : 0.003 0.026 1166 Dihedral : 20.504 99.051 2099 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.60 % Allowed : 15.53 % Favored : 82.87 % 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 aren not related in a simple way. whole: 0.39 (0.31), residues: 737 helix: 1.40 (0.28), residues: 358 sheet: -0.45 (0.55), residues: 85 loop : -0.92 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 474 TYR 0.018 0.002 TYR A 93 PHE 0.027 0.002 PHE A 612 TRP 0.008 0.002 TRP A 696 HIS 0.004 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 8512) covalent geometry : angle 0.57068 (11896) hydrogen bonds : bond 0.04554 ( 357) hydrogen bonds : angle 3.68026 ( 970) =============================================================================== Job complete usr+sys time: 1893.06 seconds wall clock time: 33 minutes 15.23 seconds (1995.23 seconds total)