Starting phenix.real_space_refine on Fri Jul 25 21:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9izq_61039/07_2025/9izq_61039.cif Found real_map, /net/cci-nas-00/data/ceres_data/9izq_61039/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9izq_61039/07_2025/9izq_61039.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9izq_61039/07_2025/9izq_61039.map" model { file = "/net/cci-nas-00/data/ceres_data/9izq_61039/07_2025/9izq_61039.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9izq_61039/07_2025/9izq_61039.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 5.24, per 1000 atoms: 0.64 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: 2.36 Conformation dependent library (CDL) restraints added in 734.8 milliseconds 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: 2.94 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: 3.29 Time building geometry restraints manager: 2.68 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: 0.110 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.640 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.320 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.31), 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 TRP 0.008 0.001 TRP A 696 HIS 0.003 0.001 HIS A 329 PHE 0.011 0.002 PHE A 612 TYR 0.014 0.002 TYR A 437 ARG 0.002 0.000 ARG A 697 Details of bonding type rmsd hydrogen bonds : bond 0.18919 ( 357) hydrogen bonds : angle 6.11187 ( 970) covalent geometry : bond 0.00439 ( 8512) covalent geometry : angle 0.56672 (11896) *********************** 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 : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9059 (ttt) cc_final: 0.8720 (ttm) REVERT: A 356 ASP cc_start: 0.7909 (t0) cc_final: 0.7564 (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: 0.2798 time to fit residues: 46.0824 Evaluate side-chains 83 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 82 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 68 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 20 optimal weight: 40.0000 chunk 41 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.4100 r_free = 0.4100 target = 0.176721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.127074 restraints weight = 10512.320| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.11 r_work: 0.3190 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8512 Z= 0.197 Angle : 0.550 8.547 11896 Z= 0.306 Chirality : 0.038 0.164 1350 Planarity : 0.003 0.030 1166 Dihedral : 20.648 101.776 2101 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.31 % Allowed : 12.19 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.31), residues: 737 helix: 0.64 (0.27), residues: 365 sheet: -0.29 (0.53), residues: 95 loop : -1.24 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 696 HIS 0.002 0.001 HIS A 726 PHE 0.028 0.002 PHE A 612 TYR 0.014 0.002 TYR A 93 ARG 0.002 0.000 ARG A 667 Details of bonding type rmsd hydrogen bonds : bond 0.05178 ( 357) hydrogen bonds : angle 4.22644 ( 970) covalent geometry : bond 0.00438 ( 8512) covalent geometry : angle 0.55029 (11896) *********************** 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 95 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9049 (ttt) cc_final: 0.8683 (ttm) REVERT: A 356 ASP cc_start: 0.7975 (t0) cc_final: 0.7626 (t0) REVERT: A 589 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.6741 (m-10) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 0.2002 time to fit residues: 25.5142 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 : 0.766 ------------------------------------------------------------------------------- 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 48 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 75 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 2 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 overall best weight: 4.0988 ------------------------------------------------------------------------------- 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 = 0.4094 r_free = 0.4094 target = 0.175602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126437 restraints weight = 10801.644| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.22 r_work: 0.3170 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 8512 Z= 0.242 Angle : 0.566 9.507 11896 Z= 0.311 Chirality : 0.039 0.175 1350 Planarity : 0.003 0.026 1166 Dihedral : 20.594 101.762 2101 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.32 % Allowed : 12.34 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.31), residues: 737 helix: 0.68 (0.27), residues: 367 sheet: -0.40 (0.52), residues: 95 loop : -1.26 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 696 HIS 0.004 0.001 HIS A 76 PHE 0.015 0.002 PHE A 7 TYR 0.015 0.002 TYR A 93 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.05133 ( 357) hydrogen bonds : angle 4.03298 ( 970) covalent geometry : bond 0.00548 ( 8512) covalent geometry : angle 0.56590 (11896) *********************** 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 97 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8992 (ttt) cc_final: 0.8722 (ttm) REVERT: A 356 ASP cc_start: 0.8069 (t0) cc_final: 0.7758 (t0) REVERT: A 588 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8880 (mppt) REVERT: A 694 GLU cc_start: 0.8045 (mp0) cc_final: 0.7819 (mp0) outliers start: 16 outliers final: 9 residues processed: 90 average time/residue: 0.2050 time to fit residues: 25.5176 Evaluate side-chains 77 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 346 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 76 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 19 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4107 r_free = 0.4107 target = 0.176743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.126778 restraints weight = 10727.861| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.10 r_work: 0.3206 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 8512 Z= 0.189 Angle : 0.521 9.249 11896 Z= 0.292 Chirality : 0.038 0.157 1350 Planarity : 0.003 0.025 1166 Dihedral : 20.504 101.180 2099 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.45 % Allowed : 13.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.31), residues: 737 helix: 0.87 (0.28), residues: 366 sheet: -0.45 (0.52), residues: 95 loop : -1.15 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 696 HIS 0.003 0.001 HIS A 76 PHE 0.023 0.002 PHE A 612 TYR 0.013 0.002 TYR A 93 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04551 ( 357) hydrogen bonds : angle 3.86998 ( 970) covalent geometry : bond 0.00427 ( 8512) covalent geometry : angle 0.52134 (11896) *********************** 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 87 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8980 (ttt) cc_final: 0.8731 (ttm) REVERT: A 356 ASP cc_start: 0.8083 (t0) cc_final: 0.7798 (t0) REVERT: A 458 MET cc_start: 0.8270 (tpt) cc_final: 0.8031 (tpp) REVERT: A 588 LYS cc_start: 0.9092 (mmtt) cc_final: 0.8819 (mppt) outliers start: 10 outliers final: 10 residues processed: 82 average time/residue: 0.2153 time to fit residues: 24.2959 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 : 0.843 ------------------------------------------------------------------------------- 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 488 GLU 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 74 optimal weight: 10.0000 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 537 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.174249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.125518 restraints weight = 10545.337| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.02 r_work: 0.3152 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 8512 Z= 0.273 Angle : 0.586 8.898 11896 Z= 0.320 Chirality : 0.041 0.177 1350 Planarity : 0.003 0.024 1166 Dihedral : 20.523 102.041 2099 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.74 % Allowed : 14.80 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.31), residues: 737 helix: 0.68 (0.27), residues: 370 sheet: -0.65 (0.53), residues: 85 loop : -1.23 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 696 HIS 0.004 0.001 HIS A 76 PHE 0.022 0.002 PHE A 612 TYR 0.017 0.002 TYR A 93 ARG 0.003 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.05125 ( 357) hydrogen bonds : angle 3.92901 ( 970) covalent geometry : bond 0.00623 ( 8512) covalent geometry : angle 0.58600 (11896) *********************** 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 87 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8979 (ttt) cc_final: 0.8688 (ttm) REVERT: A 155 MET cc_start: 0.8373 (tpp) cc_final: 0.8133 (tpp) REVERT: A 218 GLN cc_start: 0.7886 (mm-40) cc_final: 0.7620 (mm-40) REVERT: A 356 ASP cc_start: 0.8115 (t0) cc_final: 0.7841 (t0) REVERT: A 458 MET cc_start: 0.8320 (tpt) cc_final: 0.8093 (tpp) REVERT: A 588 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8804 (mppt) outliers start: 12 outliers final: 10 residues processed: 83 average time/residue: 0.2043 time to fit residues: 23.7705 Evaluate side-chains 78 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 378 THR Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 606 MET 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 15 optimal weight: 40.0000 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4129 r_free = 0.4129 target = 0.179022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.130364 restraints weight = 10686.145| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.21 r_work: 0.3228 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8512 Z= 0.128 Angle : 0.493 8.911 11896 Z= 0.274 Chirality : 0.036 0.144 1350 Planarity : 0.003 0.024 1166 Dihedral : 20.367 99.696 2099 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.45 % Allowed : 15.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.31), residues: 737 helix: 1.27 (0.28), residues: 361 sheet: -0.34 (0.57), residues: 78 loop : -1.04 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 696 HIS 0.001 0.000 HIS A 76 PHE 0.022 0.002 PHE A 480 TYR 0.011 0.001 TYR A 23 ARG 0.001 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 357) hydrogen bonds : angle 3.67450 ( 970) covalent geometry : bond 0.00280 ( 8512) covalent geometry : angle 0.49298 (11896) *********************** 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 95 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 9 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8756 (t) REVERT: A 63 MET cc_start: 0.9027 (ttt) cc_final: 0.8776 (ttm) REVERT: A 218 GLN cc_start: 0.7839 (mm-40) cc_final: 0.7563 (mm-40) REVERT: A 458 MET cc_start: 0.8327 (tpt) cc_final: 0.8111 (tpp) REVERT: A 588 LYS cc_start: 0.9101 (mmtt) cc_final: 0.8827 (mppt) REVERT: A 621 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8578 (tt) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 0.2135 time to fit residues: 27.0361 Evaluate side-chains 80 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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 589 TYR Chi-restraints excluded: chain A residue 621 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 6 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 11 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.176987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127334 restraints weight = 10680.780| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.25 r_work: 0.3200 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8512 Z= 0.220 Angle : 0.556 8.643 11896 Z= 0.304 Chirality : 0.039 0.165 1350 Planarity : 0.003 0.024 1166 Dihedral : 20.383 100.208 2099 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.60 % Allowed : 15.38 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.31), residues: 737 helix: 0.99 (0.28), residues: 367 sheet: -0.55 (0.54), residues: 85 loop : -1.16 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 696 HIS 0.004 0.001 HIS A 76 PHE 0.024 0.002 PHE A 480 TYR 0.016 0.002 TYR A 93 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 357) hydrogen bonds : angle 3.76336 ( 970) covalent geometry : bond 0.00503 ( 8512) covalent geometry : angle 0.55553 (11896) *********************** 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 84 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 63 MET cc_start: 0.8911 (ttt) cc_final: 0.8626 (ttm) REVERT: A 218 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7573 (mm-40) REVERT: A 356 ASP cc_start: 0.8054 (t0) cc_final: 0.7781 (t0) REVERT: A 458 MET cc_start: 0.8282 (tpt) cc_final: 0.8058 (tpp) REVERT: A 588 LYS cc_start: 0.9116 (mmtt) cc_final: 0.8819 (mppt) REVERT: A 621 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8646 (tt) REVERT: A 706 LYS cc_start: 0.7713 (ptmm) cc_final: 0.7488 (ptmm) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.1920 time to fit residues: 22.1901 Evaluate side-chains 78 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 69 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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 346 ILE Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 621 LEU 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 4 optimal weight: 0.2980 chunk 30 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 22 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- 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 = 0.4108 r_free = 0.4108 target = 0.177163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.128386 restraints weight = 10785.213| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.03 r_work: 0.3181 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 8512 Z= 0.200 Angle : 0.542 8.819 11896 Z= 0.298 Chirality : 0.038 0.161 1350 Planarity : 0.003 0.023 1166 Dihedral : 20.374 100.082 2099 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.74 % Allowed : 14.95 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.31), residues: 737 helix: 1.01 (0.27), residues: 367 sheet: -0.50 (0.57), residues: 78 loop : -1.19 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 696 HIS 0.003 0.001 HIS A 76 PHE 0.025 0.002 PHE A 480 TYR 0.015 0.002 TYR A 93 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 357) hydrogen bonds : angle 3.71053 ( 970) covalent geometry : bond 0.00456 ( 8512) covalent geometry : angle 0.54245 (11896) *********************** 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 86 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8926 (ttt) cc_final: 0.8664 (ttm) REVERT: A 155 MET cc_start: 0.8084 (tpp) cc_final: 0.7805 (tpt) REVERT: A 218 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7587 (mm-40) REVERT: A 356 ASP cc_start: 0.8065 (t0) cc_final: 0.7796 (t0) REVERT: A 458 MET cc_start: 0.8250 (tpt) cc_final: 0.8036 (tpp) REVERT: A 588 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8834 (mppt) REVERT: A 621 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8715 (tt) REVERT: A 706 LYS cc_start: 0.7708 (ptmm) cc_final: 0.7478 (ptmm) outliers start: 12 outliers final: 11 residues processed: 83 average time/residue: 0.1896 time to fit residues: 22.3976 Evaluate side-chains 82 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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 295 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 43 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.175986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.126724 restraints weight = 10832.459| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.04 r_work: 0.3165 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 8512 Z= 0.246 Angle : 0.582 9.022 11896 Z= 0.316 Chirality : 0.040 0.166 1350 Planarity : 0.003 0.025 1166 Dihedral : 20.418 100.620 2099 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.74 % Allowed : 15.53 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.31), residues: 737 helix: 0.95 (0.27), residues: 365 sheet: -0.64 (0.56), residues: 78 loop : -1.19 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 696 HIS 0.004 0.001 HIS A 76 PHE 0.027 0.002 PHE A 480 TYR 0.016 0.002 TYR A 93 ARG 0.002 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.04807 ( 357) hydrogen bonds : angle 3.79243 ( 970) covalent geometry : bond 0.00566 ( 8512) covalent geometry : angle 0.58177 (11896) *********************** 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: 12 poor density : 73 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.8926 (ttt) cc_final: 0.8663 (ttm) REVERT: A 155 MET cc_start: 0.8111 (tpp) cc_final: 0.7800 (tpt) REVERT: A 218 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7685 (mm-40) REVERT: A 356 ASP cc_start: 0.8061 (t0) cc_final: 0.7789 (t0) REVERT: A 458 MET cc_start: 0.8268 (tpt) cc_final: 0.8052 (tpp) REVERT: A 588 LYS cc_start: 0.9121 (mmtt) cc_final: 0.8831 (mppt) REVERT: A 621 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8727 (tt) REVERT: A 706 LYS cc_start: 0.7700 (ptmm) cc_final: 0.7463 (ptmm) outliers start: 12 outliers final: 9 residues processed: 81 average time/residue: 0.2009 time to fit residues: 22.8512 Evaluate side-chains 79 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL 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 295 ILE Chi-restraints excluded: chain A residue 589 TYR Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain A residue 711 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 79 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 78 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 = 0.178476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.129158 restraints weight = 10659.320| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.16 r_work: 0.3212 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8512 Z= 0.134 Angle : 0.529 8.457 11896 Z= 0.290 Chirality : 0.037 0.137 1350 Planarity : 0.003 0.024 1166 Dihedral : 20.407 99.701 2099 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.16 % Allowed : 15.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.31), residues: 737 helix: 1.22 (0.28), residues: 364 sheet: -0.46 (0.57), residues: 78 loop : -1.12 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 268 HIS 0.002 0.001 HIS A 76 PHE 0.026 0.002 PHE A 480 TYR 0.012 0.001 TYR A 23 ARG 0.002 0.000 ARG A 390 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 357) hydrogen bonds : angle 3.66771 ( 970) covalent geometry : bond 0.00296 ( 8512) covalent geometry : angle 0.52908 (11896) ********************** 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 81 residues out of total 689 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 MET cc_start: 0.9015 (ttt) cc_final: 0.8761 (ttm) REVERT: A 155 MET cc_start: 0.8120 (tpp) cc_final: 0.7809 (tpt) REVERT: A 458 MET cc_start: 0.8264 (tpt) cc_final: 0.8053 (tpp) REVERT: A 588 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8818 (mppt) REVERT: A 621 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8585 (tt) REVERT: A 706 LYS cc_start: 0.7683 (ptmm) cc_final: 0.7461 (ptmm) outliers start: 8 outliers final: 5 residues processed: 79 average time/residue: 0.1927 time to fit residues: 21.7457 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 : 0.757 ------------------------------------------------------------------------------- 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 216 ILE Chi-restraints excluded: chain A residue 346 ILE 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 29 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 7 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- 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 ** 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 = 0.4087 r_free = 0.4087 target = 0.175301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126029 restraints weight = 10801.262| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.04 r_work: 0.3153 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 8512 Z= 0.281 Angle : 0.602 8.475 11896 Z= 0.325 Chirality : 0.041 0.179 1350 Planarity : 0.003 0.029 1166 Dihedral : 20.607 101.044 2099 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.02 % Allowed : 15.97 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.31), residues: 737 helix: 0.97 (0.27), residues: 368 sheet: -0.74 (0.54), residues: 85 loop : -1.11 (0.36), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 696 HIS 0.004 0.001 HIS A 76 PHE 0.028 0.003 PHE A 480 TYR 0.018 0.002 TYR A 93 ARG 0.003 0.000 ARG A 280 Details of bonding type rmsd hydrogen bonds : bond 0.05020 ( 357) hydrogen bonds : angle 3.81530 ( 970) covalent geometry : bond 0.00644 ( 8512) covalent geometry : angle 0.60183 (11896) =============================================================================== Job complete usr+sys time: 4163.56 seconds wall clock time: 72 minutes 35.08 seconds (4355.08 seconds total)