Starting phenix.real_space_refine on Tue Jun 10 01:29:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7syf_25524/06_2025/7syf_25524.cif Found real_map, /net/cci-nas-00/data/ceres_data/7syf_25524/06_2025/7syf_25524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7syf_25524/06_2025/7syf_25524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7syf_25524/06_2025/7syf_25524.map" model { file = "/net/cci-nas-00/data/ceres_data/7syf_25524/06_2025/7syf_25524.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7syf_25524/06_2025/7syf_25524.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.092 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: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 7024 2.51 5 N 1942 2.21 5 O 2070 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11108 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 11108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1391, 11108 Classifications: {'peptide': 1391} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 47, 'TRANS': 1340} Chain breaks: 7 Time building chain proxies: 6.73, per 1000 atoms: 0.61 Number of scatterers: 11108 At special positions: 0 Unit cell: (111.688, 123.799, 139.947, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 2070 8.00 N 1942 7.00 C 7024 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: 2.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2636 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 7 sheets defined 58.6% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 42 through 82 removed outlier: 3.715A pdb=" N HIS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASN A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 121 removed outlier: 3.511A pdb=" N SER A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ASN A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 143 removed outlier: 4.282A pdb=" N ASP A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LYS A 141 " --> pdb=" O LYS A 137 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N CYS A 143 " --> pdb=" O LYS A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 165 removed outlier: 3.780A pdb=" N TYR A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU A 153 " --> pdb=" O CYS A 149 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 161 " --> pdb=" O ARG A 157 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 180 removed outlier: 3.673A pdb=" N MET A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 193 through 213 Proline residue: A 203 - end of helix removed outlier: 3.667A pdb=" N ARG A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 237 removed outlier: 4.610A pdb=" N ALA A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE A 237 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 256 removed outlier: 3.709A pdb=" N LEU A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 269 removed outlier: 3.646A pdb=" N ILE A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 421 Processing helix chain 'A' and resid 444 through 454 Processing helix chain 'A' and resid 459 through 473 removed outlier: 3.539A pdb=" N GLY A 463 " --> pdb=" O LYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 523 removed outlier: 3.512A pdb=" N ASP A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 510 " --> pdb=" O GLU A 506 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 512 " --> pdb=" O GLU A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 560 through 574 Processing helix chain 'A' and resid 596 through 603 removed outlier: 3.906A pdb=" N MET A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 610 Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 675 through 679 Processing helix chain 'A' and resid 680 through 694 removed outlier: 3.515A pdb=" N SER A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 744 Processing helix chain 'A' and resid 763 through 769 Processing helix chain 'A' and resid 771 through 778 Processing helix chain 'A' and resid 779 through 782 removed outlier: 4.135A pdb=" N LEU A 782 " --> pdb=" O GLU A 779 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 779 through 782' Processing helix chain 'A' and resid 791 through 806 Processing helix chain 'A' and resid 878 through 908 Processing helix chain 'A' and resid 913 through 946 Processing helix chain 'A' and resid 963 through 968 Processing helix chain 'A' and resid 1064 through 1068 Processing helix chain 'A' and resid 1069 through 1108 removed outlier: 3.622A pdb=" N ARG A1073 " --> pdb=" O LYS A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1213 through 1237 removed outlier: 4.925A pdb=" N LEU A1235 " --> pdb=" O SER A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1248 Processing helix chain 'A' and resid 1256 through 1263 Processing helix chain 'A' and resid 1263 through 1281 Processing helix chain 'A' and resid 1284 through 1315 Processing helix chain 'A' and resid 1316 through 1346 Processing helix chain 'A' and resid 1353 through 1357 removed outlier: 3.565A pdb=" N GLU A1357 " --> pdb=" O GLY A1354 " (cutoff:3.500A) Processing helix chain 'A' and resid 1359 through 1375 Processing helix chain 'A' and resid 1389 through 1407 removed outlier: 4.241A pdb=" N VAL A1401 " --> pdb=" O GLU A1397 " (cutoff:3.500A) Processing helix chain 'A' and resid 1444 through 1450 Processing helix chain 'A' and resid 1452 through 1457 Processing helix chain 'A' and resid 1480 through 1517 Processing helix chain 'A' and resid 1521 through 1551 removed outlier: 4.216A pdb=" N ARG A1534 " --> pdb=" O ASP A1530 " (cutoff:3.500A) Proline residue: A1535 - end of helix Processing helix chain 'A' and resid 1563 through 1576 Processing helix chain 'A' and resid 1588 through 1606 Processing helix chain 'A' and resid 1609 through 1611 No H-bonds generated for 'chain 'A' and resid 1609 through 1611' Processing helix chain 'A' and resid 1612 through 1624 Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 4.133A pdb=" N LEU A1630 " --> pdb=" O ARG A1626 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 257 through 258 removed outlier: 3.559A pdb=" N PHE A 327 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N PHE A 327 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LYS A 302 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLN A 287 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU A 279 " --> pdb=" O GLN A 287 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG A 289 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N THR A 277 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE A 291 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN A 275 " --> pdb=" O PHE A 291 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU A 293 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 429 through 431 removed outlier: 5.299A pdb=" N LYS A 429 " --> pdb=" O LYS A 440 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 440 " --> pdb=" O LYS A 429 " (cutoff:3.500A) removed outlier: 8.715A pdb=" N LYS A 440 " --> pdb=" O PHE A 494 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N PHE A 494 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 530 through 533 removed outlier: 5.048A pdb=" N ARG A 532 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N LYS A 540 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N SER A 541 " --> pdb=" O PHE A 595 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N PHE A 595 " --> pdb=" O SER A 541 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 668 through 671 removed outlier: 6.337A pdb=" N LEU A 701 " --> pdb=" O TYR A 669 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE A 671 " --> pdb=" O ARG A 699 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG A 699 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE A 615 " --> pdb=" O VAL A 860 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A 860 " --> pdb=" O PHE A 615 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU A 617 " --> pdb=" O GLU A 858 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N GLU A 858 " --> pdb=" O LEU A 617 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU A 619 " --> pdb=" O VAL A 856 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N HIS A 868 " --> pdb=" O SER A 980 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A1579 " --> pdb=" O CYS A1021 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N CYS A1583 " --> pdb=" O MET A1025 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N VAL A1376 " --> pdb=" O HIS A1464 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ALA A1466 " --> pdb=" O VAL A1376 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A1378 " --> pdb=" O ALA A1466 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE A1468 " --> pdb=" O LEU A1378 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N CYS A1380 " --> pdb=" O PHE A1468 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A1410 " --> pdb=" O VAL A1439 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N PHE A1441 " --> pdb=" O THR A1410 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N SER A1412 " --> pdb=" O PHE A1441 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N LEU A1443 " --> pdb=" O SER A1412 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LYS A1414 " --> pdb=" O LEU A1443 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 637 through 642 removed outlier: 6.651A pdb=" N ASP A 638 " --> pdb=" O LYS A 649 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 707 through 713 removed outlier: 6.485A pdb=" N THR A 843 " --> pdb=" O VAL A 754 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL A 754 " --> pdb=" O THR A 843 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 845 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 721 through 724 removed outlier: 6.672A pdb=" N GLN A 722 " --> pdb=" O TYR A 732 " (cutoff:3.500A) 691 hydrogen bonds defined for protein. 2007 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.33 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2166 1.32 - 1.45: 2626 1.45 - 1.57: 6413 1.57 - 1.70: 0 1.70 - 1.83: 105 Bond restraints: 11310 Sorted by residual: bond pdb=" C PHE A1260 " pdb=" N LYS A1261 " ideal model delta sigma weight residual 1.335 1.571 -0.237 1.25e-02 6.40e+03 3.59e+02 bond pdb=" C ARG A 181 " pdb=" N LYS A 182 " ideal model delta sigma weight residual 1.331 1.490 -0.159 1.42e-02 4.96e+03 1.25e+02 bond pdb=" C GLU A 619 " pdb=" N ASN A 620 " ideal model delta sigma weight residual 1.330 1.253 0.077 1.38e-02 5.25e+03 3.14e+01 bond pdb=" C VAL A 618 " pdb=" N GLU A 619 " ideal model delta sigma weight residual 1.332 1.260 0.072 1.40e-02 5.10e+03 2.66e+01 bond pdb=" C LEU A 227 " pdb=" N GLN A 228 " ideal model delta sigma weight residual 1.335 1.387 -0.053 1.31e-02 5.83e+03 1.61e+01 ... (remaining 11305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 11715 2.17 - 4.33: 3173 4.33 - 6.50: 338 6.50 - 8.67: 28 8.67 - 10.83: 8 Bond angle restraints: 15262 Sorted by residual: angle pdb=" C PHE A1260 " pdb=" N LYS A1261 " pdb=" CA LYS A1261 " ideal model delta sigma weight residual 120.54 109.71 10.83 1.35e+00 5.49e-01 6.44e+01 angle pdb=" N TYR A 539 " pdb=" CA TYR A 539 " pdb=" C TYR A 539 " ideal model delta sigma weight residual 109.95 99.43 10.52 1.59e+00 3.96e-01 4.38e+01 angle pdb=" CA PHE A 70 " pdb=" CB PHE A 70 " pdb=" CG PHE A 70 " ideal model delta sigma weight residual 113.80 120.01 -6.21 1.00e+00 1.00e+00 3.86e+01 angle pdb=" N ILE A 103 " pdb=" CA ILE A 103 " pdb=" CB ILE A 103 " ideal model delta sigma weight residual 110.51 117.25 -6.74 1.11e+00 8.12e-01 3.69e+01 angle pdb=" O PHE A1260 " pdb=" C PHE A1260 " pdb=" N LYS A1261 " ideal model delta sigma weight residual 122.12 128.45 -6.33 1.06e+00 8.90e-01 3.57e+01 ... (remaining 15257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 6298 17.72 - 35.44: 481 35.44 - 53.15: 99 53.15 - 70.87: 35 70.87 - 88.59: 11 Dihedral angle restraints: 6924 sinusoidal: 2859 harmonic: 4065 Sorted by residual: dihedral pdb=" CA LEU A1068 " pdb=" C LEU A1068 " pdb=" N LYS A1069 " pdb=" CA LYS A1069 " ideal model delta harmonic sigma weight residual 180.00 150.57 29.43 0 5.00e+00 4.00e-02 3.46e+01 dihedral pdb=" CA LEU A 700 " pdb=" C LEU A 700 " pdb=" N LEU A 701 " pdb=" CA LEU A 701 " ideal model delta harmonic sigma weight residual 180.00 150.98 29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ALA A 283 " pdb=" C ALA A 283 " pdb=" N GLY A 284 " pdb=" CA GLY A 284 " ideal model delta harmonic sigma weight residual -180.00 -151.65 -28.35 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 6921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1210 0.098 - 0.196: 426 0.196 - 0.294: 56 0.294 - 0.392: 11 0.392 - 0.490: 6 Chirality restraints: 1709 Sorted by residual: chirality pdb=" CA ILE A 103 " pdb=" N ILE A 103 " pdb=" C ILE A 103 " pdb=" CB ILE A 103 " both_signs ideal model delta sigma weight residual False 2.43 1.94 0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" CA ARG A 303 " pdb=" N ARG A 303 " pdb=" C ARG A 303 " pdb=" CB ARG A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CA ARG A 198 " pdb=" N ARG A 198 " pdb=" C ARG A 198 " pdb=" CB ARG A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.26e+00 ... (remaining 1706 not shown) Planarity restraints: 1973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 260 " -0.134 2.00e-02 2.50e+03 7.38e-02 1.36e+02 pdb=" CG TRP A 260 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP A 260 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP A 260 " 0.108 2.00e-02 2.50e+03 pdb=" NE1 TRP A 260 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 260 " 0.038 2.00e-02 2.50e+03 pdb=" CE3 TRP A 260 " 0.102 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 260 " -0.028 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 260 " -0.020 2.00e-02 2.50e+03 pdb=" CH2 TRP A 260 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 787 " -0.093 2.00e-02 2.50e+03 5.11e-02 6.52e+01 pdb=" CG TRP A 787 " 0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP A 787 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TRP A 787 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP A 787 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP A 787 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP A 787 " 0.074 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 787 " -0.064 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 787 " 0.031 2.00e-02 2.50e+03 pdb=" CH2 TRP A 787 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A1020 " 0.084 2.00e-02 2.50e+03 6.25e-02 5.85e+01 pdb=" CG HIS A1020 " -0.095 2.00e-02 2.50e+03 pdb=" ND1 HIS A1020 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 HIS A1020 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 HIS A1020 " 0.034 2.00e-02 2.50e+03 pdb=" NE2 HIS A1020 " 0.055 2.00e-02 2.50e+03 ... (remaining 1970 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 4664 2.95 - 3.44: 11727 3.44 - 3.92: 18891 3.92 - 4.41: 21061 4.41 - 4.90: 34498 Nonbonded interactions: 90841 Sorted by model distance: nonbonded pdb=" N TYR A 539 " pdb=" O TYR A 539 " model vdw 2.460 2.496 nonbonded pdb=" OG SER A 458 " pdb=" OE2 GLU A 462 " model vdw 2.478 3.040 nonbonded pdb=" OG SER A1569 " pdb=" OE2 GLU A1597 " model vdw 2.512 3.040 nonbonded pdb=" ND1 HIS A 77 " pdb=" NH2 ARG A 80 " model vdw 2.520 3.200 nonbonded pdb=" OG1 THR A 354 " pdb=" OE1 GLU A1092 " model vdw 2.564 3.040 ... (remaining 90836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 0.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 29.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6223 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 : 0.013 0.237 11310 Z= 0.818 Angle : 1.861 10.834 15262 Z= 1.269 Chirality : 0.098 0.490 1709 Planarity : 0.015 0.128 1973 Dihedral : 14.320 88.585 4288 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.31 % Allowed : 3.60 % Favored : 95.09 % Cbeta Deviations : 0.61 % Peptide Plane: Cis-proline : 6.00 % 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: -1.56 (0.20), residues: 1375 helix: -1.07 (0.15), residues: 766 sheet: -0.80 (0.39), residues: 153 loop : -0.65 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.032 TRP A 260 HIS 0.019 0.005 HIS A 579 PHE 0.067 0.014 PHE A 593 TYR 0.097 0.016 TYR A 191 ARG 0.009 0.001 ARG A 212 Details of bonding type rmsd hydrogen bonds : bond 0.16062 ( 691) hydrogen bonds : angle 7.53870 ( 2007) covalent geometry : bond 0.01269 (11310) covalent geometry : angle 1.86146 (15262) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 409 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8209 (pp30) REVERT: A 104 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8566 (pt0) REVERT: A 112 ASP cc_start: 0.8719 (m-30) cc_final: 0.8507 (t0) REVERT: A 144 VAL cc_start: 0.8328 (m) cc_final: 0.7645 (p) REVERT: A 176 MET cc_start: 0.6393 (mtm) cc_final: 0.5915 (ttt) REVERT: A 177 LEU cc_start: 0.2601 (OUTLIER) cc_final: 0.1563 (mt) REVERT: A 230 MET cc_start: 0.7197 (mmp) cc_final: 0.6594 (mmp) REVERT: A 292 PHE cc_start: 0.6897 (m-80) cc_final: 0.6467 (m-80) REVERT: A 359 TRP cc_start: 0.6886 (p90) cc_final: 0.6224 (p90) REVERT: A 370 PHE cc_start: 0.7952 (p90) cc_final: 0.7621 (p90) REVERT: A 510 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5527 (tt) REVERT: A 511 MET cc_start: 0.5830 (mpp) cc_final: 0.4848 (mpp) REVERT: A 539 TYR cc_start: 0.7354 (m-80) cc_final: 0.6967 (m-80) REVERT: A 591 GLN cc_start: 0.7824 (mt0) cc_final: 0.6737 (tt0) REVERT: A 598 ASP cc_start: 0.8273 (m-30) cc_final: 0.7583 (m-30) REVERT: A 622 LEU cc_start: 0.7602 (tp) cc_final: 0.7060 (tp) REVERT: A 631 GLN cc_start: 0.7013 (mt0) cc_final: 0.6457 (mt0) REVERT: A 691 SER cc_start: 0.6742 (m) cc_final: 0.6485 (p) REVERT: A 701 LEU cc_start: 0.7785 (mt) cc_final: 0.7475 (mm) REVERT: A 741 MET cc_start: 0.7502 (ttm) cc_final: 0.6183 (ttm) REVERT: A 768 LEU cc_start: 0.8776 (mt) cc_final: 0.8521 (mt) REVERT: A 770 HIS cc_start: 0.8372 (m-70) cc_final: 0.7852 (m-70) REVERT: A 900 ASN cc_start: 0.8730 (m-40) cc_final: 0.8324 (t0) REVERT: A 915 PRO cc_start: 0.6507 (Cg_exo) cc_final: 0.5512 (Cg_endo) REVERT: A 919 PHE cc_start: 0.7522 (t80) cc_final: 0.7114 (t80) REVERT: A 922 ILE cc_start: 0.8722 (mt) cc_final: 0.8076 (mt) REVERT: A 923 CYS cc_start: 0.7634 (m) cc_final: 0.6920 (m) REVERT: A 924 ASP cc_start: 0.8929 (m-30) cc_final: 0.8714 (m-30) REVERT: A 925 THR cc_start: 0.8956 (m) cc_final: 0.8750 (p) REVERT: A 926 LYS cc_start: 0.8618 (mttt) cc_final: 0.8282 (mttt) REVERT: A 928 GLU cc_start: 0.8744 (tt0) cc_final: 0.8490 (tt0) REVERT: A 929 SER cc_start: 0.9131 (t) cc_final: 0.8915 (p) REVERT: A 932 GLN cc_start: 0.8093 (mt0) cc_final: 0.7501 (tp-100) REVERT: A 936 CYS cc_start: 0.8731 (m) cc_final: 0.7422 (m) REVERT: A 939 GLU cc_start: 0.7806 (tp30) cc_final: 0.6874 (tp30) REVERT: A 940 PHE cc_start: 0.8560 (m-10) cc_final: 0.7669 (m-10) REVERT: A 943 GLN cc_start: 0.7534 (mt0) cc_final: 0.6308 (mt0) REVERT: A 1079 TYR cc_start: 0.6817 (m-10) cc_final: 0.6307 (m-10) REVERT: A 1104 LEU cc_start: 0.6206 (mt) cc_final: 0.5570 (tt) REVERT: A 1214 LYS cc_start: 0.8444 (mttt) cc_final: 0.7990 (mtmm) REVERT: A 1324 ASP cc_start: 0.8176 (m-30) cc_final: 0.7700 (m-30) REVERT: A 1328 CYS cc_start: 0.6946 (t) cc_final: 0.6187 (t) REVERT: A 1332 VAL cc_start: 0.9021 (t) cc_final: 0.8336 (t) REVERT: A 1339 SER cc_start: 0.9047 (t) cc_final: 0.8674 (p) REVERT: A 1343 LEU cc_start: 0.8889 (mt) cc_final: 0.8673 (mm) REVERT: A 1353 ASN cc_start: 0.6419 (m-40) cc_final: 0.6006 (m-40) REVERT: A 1366 LYS cc_start: 0.8935 (mttt) cc_final: 0.8546 (mttt) REVERT: A 1369 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8224 (mt-10) REVERT: A 1378 LEU cc_start: 0.7679 (tp) cc_final: 0.7399 (tp) REVERT: A 1384 LEU cc_start: 0.8469 (mt) cc_final: 0.7496 (mp) REVERT: A 1414 LYS cc_start: 0.7917 (mttt) cc_final: 0.7283 (mmmm) REVERT: A 1428 TYR cc_start: 0.7256 (m-80) cc_final: 0.6753 (m-80) REVERT: A 1438 LYS cc_start: 0.8282 (ttpt) cc_final: 0.8072 (ttpp) REVERT: A 1441 PHE cc_start: 0.8074 (m-80) cc_final: 0.6516 (m-80) REVERT: A 1504 TYR cc_start: 0.8498 (t80) cc_final: 0.8224 (t80) REVERT: A 1507 LYS cc_start: 0.8570 (mttt) cc_final: 0.8259 (tptt) REVERT: A 1508 LEU cc_start: 0.8727 (tp) cc_final: 0.7579 (tp) REVERT: A 1512 TYR cc_start: 0.7252 (m-80) cc_final: 0.6748 (m-80) REVERT: A 1530 ASP cc_start: 0.6688 (m-30) cc_final: 0.6472 (m-30) REVERT: A 1531 GLN cc_start: 0.8564 (mt0) cc_final: 0.7799 (mm110) REVERT: A 1536 ILE cc_start: 0.8915 (mt) cc_final: 0.8461 (tp) REVERT: A 1542 LEU cc_start: 0.9254 (mt) cc_final: 0.8986 (mt) REVERT: A 1546 MET cc_start: 0.8415 (tpp) cc_final: 0.8097 (mmm) REVERT: A 1593 SER cc_start: 0.7864 (t) cc_final: 0.7654 (p) REVERT: A 1605 SER cc_start: 0.8432 (m) cc_final: 0.7977 (p) REVERT: A 1633 ASN cc_start: 0.8377 (m-40) cc_final: 0.7311 (m-40) outliers start: 16 outliers final: 3 residues processed: 418 average time/residue: 0.3310 time to fit residues: 184.4541 Evaluate side-chains 295 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 290 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 42 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 81 optimal weight: 0.1980 chunk 126 optimal weight: 1.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 110 HIS A 228 GLN A 243 GLN A 256 HIS A 393 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 578 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN A 722 GLN A 790 HIS A1370 GLN A1379 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.140206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.121790 restraints weight = 32696.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.125074 restraints weight = 21087.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.127365 restraints weight = 14791.827| |-----------------------------------------------------------------------------| r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11310 Z= 0.177 Angle : 0.686 9.758 15262 Z= 0.369 Chirality : 0.044 0.238 1709 Planarity : 0.005 0.082 1973 Dihedral : 6.128 75.911 1510 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.33 % Allowed : 3.68 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.50 (0.22), residues: 1375 helix: 0.90 (0.18), residues: 768 sheet: -0.67 (0.36), residues: 173 loop : -0.03 (0.32), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP A 369 HIS 0.007 0.001 HIS A 110 PHE 0.027 0.002 PHE A 70 TYR 0.032 0.002 TYR A1096 ARG 0.012 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.05349 ( 691) hydrogen bonds : angle 5.23123 ( 2007) covalent geometry : bond 0.00372 (11310) covalent geometry : angle 0.68628 (15262) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 319 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.7228 (mp) cc_final: 0.6804 (pp) REVERT: A 72 GLN cc_start: 0.8348 (tm-30) cc_final: 0.8008 (tm-30) REVERT: A 104 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8102 (mp0) REVERT: A 108 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7999 (pm20) REVERT: A 176 MET cc_start: 0.6833 (mtm) cc_final: 0.6333 (ttt) REVERT: A 353 TYR cc_start: 0.8337 (m-80) cc_final: 0.8096 (m-10) REVERT: A 359 TRP cc_start: 0.6458 (p90) cc_final: 0.5942 (p90) REVERT: A 372 CYS cc_start: 0.8222 (m) cc_final: 0.7936 (t) REVERT: A 373 MET cc_start: 0.6679 (mpp) cc_final: 0.6079 (mpp) REVERT: A 532 ARG cc_start: 0.2987 (tpt170) cc_final: 0.2433 (tpm170) REVERT: A 539 TYR cc_start: 0.7399 (m-80) cc_final: 0.7035 (m-80) REVERT: A 547 LYS cc_start: 0.7058 (mmtt) cc_final: 0.6741 (tppt) REVERT: A 586 PHE cc_start: 0.7119 (t80) cc_final: 0.6869 (t80) REVERT: A 591 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7340 (mt0) REVERT: A 598 ASP cc_start: 0.8119 (m-30) cc_final: 0.7384 (m-30) REVERT: A 691 SER cc_start: 0.6934 (m) cc_final: 0.6541 (p) REVERT: A 754 VAL cc_start: 0.8467 (m) cc_final: 0.8257 (t) REVERT: A 770 HIS cc_start: 0.8535 (m-70) cc_final: 0.7968 (m90) REVERT: A 922 ILE cc_start: 0.8699 (mt) cc_final: 0.8004 (mt) REVERT: A 926 LYS cc_start: 0.8430 (mttt) cc_final: 0.8070 (mttt) REVERT: A 928 GLU cc_start: 0.8460 (tt0) cc_final: 0.8111 (tt0) REVERT: A 932 GLN cc_start: 0.7805 (mt0) cc_final: 0.7508 (tp40) REVERT: A 936 CYS cc_start: 0.8535 (m) cc_final: 0.7907 (m) REVERT: A 939 GLU cc_start: 0.7536 (tp30) cc_final: 0.6464 (tp30) REVERT: A 940 PHE cc_start: 0.8525 (m-10) cc_final: 0.7878 (m-10) REVERT: A 943 GLN cc_start: 0.7198 (mt0) cc_final: 0.6001 (mt0) REVERT: A 977 MET cc_start: 0.7368 (ttm) cc_final: 0.7075 (ttp) REVERT: A 1022 ILE cc_start: 0.7744 (mp) cc_final: 0.7481 (mp) REVERT: A 1079 TYR cc_start: 0.6958 (m-10) cc_final: 0.6612 (m-10) REVERT: A 1104 LEU cc_start: 0.6158 (mt) cc_final: 0.5841 (tp) REVERT: A 1214 LYS cc_start: 0.8345 (mttt) cc_final: 0.7724 (pttm) REVERT: A 1233 ASN cc_start: 0.7326 (m110) cc_final: 0.7042 (m110) REVERT: A 1271 ARG cc_start: 0.8533 (mtm-85) cc_final: 0.8249 (mtp180) REVERT: A 1296 ILE cc_start: 0.9150 (mt) cc_final: 0.8948 (pt) REVERT: A 1320 GLN cc_start: 0.8477 (tp40) cc_final: 0.8067 (tp-100) REVERT: A 1324 ASP cc_start: 0.7850 (m-30) cc_final: 0.7553 (m-30) REVERT: A 1332 VAL cc_start: 0.8895 (t) cc_final: 0.8538 (t) REVERT: A 1338 PHE cc_start: 0.8365 (t80) cc_final: 0.8106 (t80) REVERT: A 1339 SER cc_start: 0.8922 (t) cc_final: 0.8339 (p) REVERT: A 1343 LEU cc_start: 0.8817 (mt) cc_final: 0.8214 (pp) REVERT: A 1352 ASN cc_start: 0.7160 (p0) cc_final: 0.6264 (p0) REVERT: A 1353 ASN cc_start: 0.5717 (m-40) cc_final: 0.5087 (m-40) REVERT: A 1366 LYS cc_start: 0.9168 (mttt) cc_final: 0.8888 (mttt) REVERT: A 1369 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8109 (mt-10) REVERT: A 1378 LEU cc_start: 0.7630 (tp) cc_final: 0.7323 (tp) REVERT: A 1403 LEU cc_start: 0.8134 (mt) cc_final: 0.7828 (mp) REVERT: A 1428 TYR cc_start: 0.7024 (m-80) cc_final: 0.6745 (m-80) REVERT: A 1438 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7944 (ttpp) REVERT: A 1441 PHE cc_start: 0.8085 (m-80) cc_final: 0.7221 (m-10) REVERT: A 1490 GLN cc_start: 0.8179 (tt0) cc_final: 0.7720 (mt0) REVERT: A 1502 GLN cc_start: 0.7996 (tm-30) cc_final: 0.7768 (tp-100) REVERT: A 1508 LEU cc_start: 0.8873 (tp) cc_final: 0.6900 (tp) REVERT: A 1530 ASP cc_start: 0.6432 (m-30) cc_final: 0.6201 (m-30) REVERT: A 1531 GLN cc_start: 0.8443 (mt0) cc_final: 0.7705 (mm110) REVERT: A 1546 MET cc_start: 0.8190 (tpp) cc_final: 0.7973 (mmm) REVERT: A 1580 MET cc_start: 0.6426 (mtp) cc_final: 0.6223 (mtp) REVERT: A 1598 GLN cc_start: 0.8269 (mt0) cc_final: 0.7882 (mt0) REVERT: A 1605 SER cc_start: 0.8447 (m) cc_final: 0.8231 (p) REVERT: A 1640 MET cc_start: 0.6778 (tpp) cc_final: 0.5837 (mmm) outliers start: 4 outliers final: 2 residues processed: 322 average time/residue: 0.2803 time to fit residues: 125.3448 Evaluate side-chains 274 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 271 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 12 optimal weight: 0.7980 chunk 128 optimal weight: 0.0020 chunk 36 optimal weight: 0.0570 chunk 48 optimal weight: 2.9990 overall best weight: 1.1710 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS A 631 GLN ** A 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN A1227 ASN A1537 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.139913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.120930 restraints weight = 33139.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.124159 restraints weight = 21837.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.126449 restraints weight = 15576.706| |-----------------------------------------------------------------------------| r_work (final): 0.4026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6350 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11310 Z= 0.155 Angle : 0.640 9.873 15262 Z= 0.338 Chirality : 0.042 0.249 1709 Planarity : 0.004 0.054 1973 Dihedral : 5.609 75.512 1510 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.08 % Allowed : 1.88 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.89 (0.23), residues: 1375 helix: 1.27 (0.18), residues: 770 sheet: -0.68 (0.37), residues: 155 loop : 0.07 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1367 HIS 0.004 0.001 HIS A 77 PHE 0.017 0.002 PHE A 370 TYR 0.024 0.002 TYR A1096 ARG 0.008 0.001 ARG A1454 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 691) hydrogen bonds : angle 4.95836 ( 2007) covalent geometry : bond 0.00327 (11310) covalent geometry : angle 0.63994 (15262) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.7090 (mp) cc_final: 0.6653 (pp) REVERT: A 72 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8111 (pp30) REVERT: A 104 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8115 (mp0) REVERT: A 176 MET cc_start: 0.6856 (mtm) cc_final: 0.6388 (ttt) REVERT: A 353 TYR cc_start: 0.8283 (m-80) cc_final: 0.8042 (m-10) REVERT: A 359 TRP cc_start: 0.6431 (p90) cc_final: 0.6227 (p90) REVERT: A 373 MET cc_start: 0.6703 (mpp) cc_final: 0.6289 (mpp) REVERT: A 430 ASP cc_start: 0.7649 (t0) cc_final: 0.7393 (m-30) REVERT: A 468 GLN cc_start: 0.6860 (tp40) cc_final: 0.5957 (pp30) REVERT: A 511 MET cc_start: 0.6146 (mpp) cc_final: 0.5747 (mmt) REVERT: A 539 TYR cc_start: 0.7504 (m-80) cc_final: 0.6956 (m-80) REVERT: A 577 MET cc_start: 0.5739 (ttp) cc_final: 0.5415 (ttp) REVERT: A 598 ASP cc_start: 0.7989 (m-30) cc_final: 0.7598 (m-30) REVERT: A 691 SER cc_start: 0.7065 (m) cc_final: 0.6692 (p) REVERT: A 711 LYS cc_start: 0.7376 (mppt) cc_final: 0.7041 (mppt) REVERT: A 741 MET cc_start: 0.7475 (mtt) cc_final: 0.6921 (mtt) REVERT: A 770 HIS cc_start: 0.8451 (m-70) cc_final: 0.7993 (m90) REVERT: A 841 MET cc_start: 0.6879 (mmt) cc_final: 0.5917 (mmm) REVERT: A 859 TYR cc_start: 0.7674 (p90) cc_final: 0.7447 (p90) REVERT: A 922 ILE cc_start: 0.8567 (mt) cc_final: 0.8292 (pt) REVERT: A 928 GLU cc_start: 0.8383 (tt0) cc_final: 0.8091 (tt0) REVERT: A 932 GLN cc_start: 0.7815 (mt0) cc_final: 0.7527 (tp40) REVERT: A 936 CYS cc_start: 0.8499 (m) cc_final: 0.8001 (m) REVERT: A 939 GLU cc_start: 0.7585 (tp30) cc_final: 0.6851 (tp30) REVERT: A 940 PHE cc_start: 0.8634 (m-10) cc_final: 0.8344 (m-10) REVERT: A 953 LYS cc_start: 0.7773 (tttt) cc_final: 0.7547 (tttt) REVERT: A 1015 MET cc_start: 0.5521 (mpp) cc_final: 0.4235 (mpp) REVERT: A 1021 CYS cc_start: 0.8036 (t) cc_final: 0.7790 (t) REVERT: A 1079 TYR cc_start: 0.6937 (m-10) cc_final: 0.6584 (m-10) REVERT: A 1104 LEU cc_start: 0.6389 (mt) cc_final: 0.6077 (tp) REVERT: A 1214 LYS cc_start: 0.8311 (mttt) cc_final: 0.7778 (pttm) REVERT: A 1229 VAL cc_start: 0.8358 (t) cc_final: 0.7698 (t) REVERT: A 1233 ASN cc_start: 0.7277 (m110) cc_final: 0.6955 (m-40) REVERT: A 1235 LEU cc_start: 0.8868 (mt) cc_final: 0.8660 (mt) REVERT: A 1250 HIS cc_start: 0.6339 (m90) cc_final: 0.5661 (m90) REVERT: A 1271 ARG cc_start: 0.8448 (mtm-85) cc_final: 0.8192 (mtp180) REVERT: A 1324 ASP cc_start: 0.7998 (m-30) cc_final: 0.7280 (m-30) REVERT: A 1339 SER cc_start: 0.8808 (t) cc_final: 0.8401 (p) REVERT: A 1343 LEU cc_start: 0.8579 (mt) cc_final: 0.8293 (pp) REVERT: A 1351 ASN cc_start: 0.7769 (t0) cc_final: 0.7397 (t0) REVERT: A 1352 ASN cc_start: 0.6985 (p0) cc_final: 0.6707 (p0) REVERT: A 1353 ASN cc_start: 0.5639 (m-40) cc_final: 0.5355 (m-40) REVERT: A 1376 VAL cc_start: 0.7862 (t) cc_final: 0.7628 (t) REVERT: A 1378 LEU cc_start: 0.7602 (tp) cc_final: 0.6865 (tp) REVERT: A 1384 LEU cc_start: 0.8403 (mt) cc_final: 0.8037 (mt) REVERT: A 1403 LEU cc_start: 0.7944 (mt) cc_final: 0.7469 (mt) REVERT: A 1463 LEU cc_start: 0.8039 (tp) cc_final: 0.7620 (mm) REVERT: A 1488 ASP cc_start: 0.7356 (m-30) cc_final: 0.7114 (m-30) REVERT: A 1502 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7708 (tp-100) REVERT: A 1530 ASP cc_start: 0.6456 (m-30) cc_final: 0.6253 (m-30) REVERT: A 1531 GLN cc_start: 0.8501 (mt0) cc_final: 0.7714 (mm110) REVERT: A 1546 MET cc_start: 0.8288 (tpp) cc_final: 0.8064 (mmm) REVERT: A 1567 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7560 (mm) REVERT: A 1580 MET cc_start: 0.6383 (mtp) cc_final: 0.5766 (mtp) outliers start: 1 outliers final: 0 residues processed: 295 average time/residue: 0.2608 time to fit residues: 105.9312 Evaluate side-chains 260 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 62 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN ** A 975 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1070 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1320 GLN ** A1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1537 ASN A1551 HIS A1633 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.132527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.114334 restraints weight = 33704.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.117418 restraints weight = 22130.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.119635 restraints weight = 15780.009| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6510 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11310 Z= 0.216 Angle : 0.696 10.008 15262 Z= 0.364 Chirality : 0.045 0.335 1709 Planarity : 0.005 0.057 1973 Dihedral : 5.784 75.446 1510 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.16 % Allowed : 3.84 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.66 (0.23), residues: 1375 helix: 1.14 (0.18), residues: 776 sheet: -0.72 (0.38), residues: 154 loop : -0.20 (0.31), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A1367 HIS 0.008 0.002 HIS A 77 PHE 0.036 0.003 PHE A 291 TYR 0.027 0.002 TYR A1428 ARG 0.010 0.001 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.04844 ( 691) hydrogen bonds : angle 5.07948 ( 2007) covalent geometry : bond 0.00447 (11310) covalent geometry : angle 0.69591 (15262) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 289 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8271 (tm-30) REVERT: A 104 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8258 (mp0) REVERT: A 257 ILE cc_start: 0.7363 (mt) cc_final: 0.6890 (mm) REVERT: A 278 LEU cc_start: 0.8387 (pp) cc_final: 0.8050 (pp) REVERT: A 353 TYR cc_start: 0.8360 (m-80) cc_final: 0.8107 (m-10) REVERT: A 355 VAL cc_start: 0.7892 (t) cc_final: 0.7578 (m) REVERT: A 360 LYS cc_start: 0.7889 (pptt) cc_final: 0.7572 (pptt) REVERT: A 430 ASP cc_start: 0.7641 (t0) cc_final: 0.7294 (m-30) REVERT: A 539 TYR cc_start: 0.7432 (m-80) cc_final: 0.6743 (m-80) REVERT: A 577 MET cc_start: 0.6258 (ttp) cc_final: 0.5946 (ttp) REVERT: A 598 ASP cc_start: 0.8045 (m-30) cc_final: 0.7309 (m-30) REVERT: A 691 SER cc_start: 0.7209 (m) cc_final: 0.6838 (p) REVERT: A 695 ARG cc_start: 0.8222 (mmp80) cc_final: 0.7874 (mmp-170) REVERT: A 722 GLN cc_start: 0.7382 (mt0) cc_final: 0.7097 (mt0) REVERT: A 741 MET cc_start: 0.7762 (mtt) cc_final: 0.7111 (mtt) REVERT: A 760 MET cc_start: 0.8092 (ttp) cc_final: 0.7621 (tpp) REVERT: A 859 TYR cc_start: 0.7789 (p90) cc_final: 0.7400 (p90) REVERT: A 928 GLU cc_start: 0.8555 (tt0) cc_final: 0.8272 (tt0) REVERT: A 932 GLN cc_start: 0.8060 (mt0) cc_final: 0.7648 (tp40) REVERT: A 936 CYS cc_start: 0.8529 (m) cc_final: 0.7902 (m) REVERT: A 939 GLU cc_start: 0.7787 (tp30) cc_final: 0.7060 (tp30) REVERT: A 1015 MET cc_start: 0.5328 (mpp) cc_final: 0.4787 (mpp) REVERT: A 1022 ILE cc_start: 0.7509 (mp) cc_final: 0.7207 (mp) REVERT: A 1079 TYR cc_start: 0.6718 (m-10) cc_final: 0.6385 (m-10) REVERT: A 1214 LYS cc_start: 0.8413 (mttt) cc_final: 0.7902 (pttm) REVERT: A 1229 VAL cc_start: 0.8220 (t) cc_final: 0.7534 (t) REVERT: A 1233 ASN cc_start: 0.7456 (m110) cc_final: 0.7075 (m-40) REVERT: A 1250 HIS cc_start: 0.6482 (m90) cc_final: 0.5742 (m90) REVERT: A 1296 ILE cc_start: 0.9182 (mt) cc_final: 0.8891 (pt) REVERT: A 1320 GLN cc_start: 0.8414 (tp40) cc_final: 0.8057 (tp40) REVERT: A 1324 ASP cc_start: 0.8039 (m-30) cc_final: 0.7350 (m-30) REVERT: A 1339 SER cc_start: 0.9026 (t) cc_final: 0.8770 (p) REVERT: A 1342 LEU cc_start: 0.8515 (tp) cc_final: 0.8237 (tp) REVERT: A 1343 LEU cc_start: 0.8680 (mt) cc_final: 0.8378 (pp) REVERT: A 1346 LEU cc_start: 0.9054 (mt) cc_final: 0.8808 (mt) REVERT: A 1351 ASN cc_start: 0.7963 (t0) cc_final: 0.7720 (t0) REVERT: A 1353 ASN cc_start: 0.5728 (m-40) cc_final: 0.5526 (m-40) REVERT: A 1357 GLU cc_start: 0.6744 (tm-30) cc_final: 0.6533 (tm-30) REVERT: A 1366 LYS cc_start: 0.9212 (mttt) cc_final: 0.8874 (mttt) REVERT: A 1376 VAL cc_start: 0.7603 (t) cc_final: 0.7346 (p) REVERT: A 1392 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6801 (mm-30) REVERT: A 1403 LEU cc_start: 0.8151 (mt) cc_final: 0.7906 (mp) REVERT: A 1407 ASP cc_start: 0.7798 (m-30) cc_final: 0.7554 (m-30) REVERT: A 1488 ASP cc_start: 0.7355 (m-30) cc_final: 0.7134 (m-30) REVERT: A 1502 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7606 (tp-100) REVERT: A 1508 LEU cc_start: 0.8845 (tp) cc_final: 0.7448 (tp) REVERT: A 1512 TYR cc_start: 0.7170 (m-80) cc_final: 0.6751 (m-80) REVERT: A 1514 GLU cc_start: 0.7753 (mp0) cc_final: 0.6992 (mp0) REVERT: A 1530 ASP cc_start: 0.6530 (m-30) cc_final: 0.6312 (m-30) REVERT: A 1531 GLN cc_start: 0.8584 (mt0) cc_final: 0.7802 (mm110) REVERT: A 1546 MET cc_start: 0.8414 (tpp) cc_final: 0.8063 (mmt) REVERT: A 1580 MET cc_start: 0.6350 (mtp) cc_final: 0.5855 (mtp) REVERT: A 1583 CYS cc_start: 0.8180 (p) cc_final: 0.7576 (p) REVERT: A 1598 GLN cc_start: 0.8194 (mt0) cc_final: 0.7630 (mt0) outliers start: 2 outliers final: 1 residues processed: 290 average time/residue: 0.2592 time to fit residues: 104.0952 Evaluate side-chains 262 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 260 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 48 optimal weight: 0.0030 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 77 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.136634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.117714 restraints weight = 32870.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.120829 restraints weight = 21494.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.123089 restraints weight = 15310.214| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6424 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11310 Z= 0.139 Angle : 0.621 8.618 15262 Z= 0.324 Chirality : 0.041 0.209 1709 Planarity : 0.005 0.102 1973 Dihedral : 5.456 74.213 1510 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.88 (0.23), residues: 1375 helix: 1.33 (0.18), residues: 784 sheet: -0.64 (0.38), residues: 154 loop : -0.16 (0.32), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 369 HIS 0.007 0.001 HIS A 578 PHE 0.020 0.002 PHE A 291 TYR 0.011 0.001 TYR A1428 ARG 0.010 0.001 ARG A1454 Details of bonding type rmsd hydrogen bonds : bond 0.04347 ( 691) hydrogen bonds : angle 4.81296 ( 2007) covalent geometry : bond 0.00291 (11310) covalent geometry : angle 0.62115 (15262) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 294 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.7109 (mt) cc_final: 0.6785 (pp) REVERT: A 164 LYS cc_start: 0.7586 (pptt) cc_final: 0.7358 (pptt) REVERT: A 175 CYS cc_start: 0.8330 (m) cc_final: 0.8128 (m) REVERT: A 278 LEU cc_start: 0.8283 (pp) cc_final: 0.7816 (pp) REVERT: A 343 ASP cc_start: 0.8315 (m-30) cc_final: 0.8032 (t0) REVERT: A 353 TYR cc_start: 0.7843 (m-80) cc_final: 0.7600 (m-10) REVERT: A 360 LYS cc_start: 0.7559 (pptt) cc_final: 0.7227 (pptt) REVERT: A 511 MET cc_start: 0.6614 (mmp) cc_final: 0.6078 (mmp) REVERT: A 539 TYR cc_start: 0.7416 (m-80) cc_final: 0.6844 (m-80) REVERT: A 577 MET cc_start: 0.5691 (ttp) cc_final: 0.5034 (ttt) REVERT: A 598 ASP cc_start: 0.7983 (m-30) cc_final: 0.7405 (m-30) REVERT: A 691 SER cc_start: 0.6938 (m) cc_final: 0.6577 (p) REVERT: A 741 MET cc_start: 0.7614 (mtt) cc_final: 0.6994 (mtt) REVERT: A 760 MET cc_start: 0.7905 (ttp) cc_final: 0.7640 (tpp) REVERT: A 841 MET cc_start: 0.6980 (mmt) cc_final: 0.6306 (mmm) REVERT: A 859 TYR cc_start: 0.7642 (p90) cc_final: 0.7389 (p90) REVERT: A 928 GLU cc_start: 0.8547 (tt0) cc_final: 0.8239 (tt0) REVERT: A 932 GLN cc_start: 0.7899 (mt0) cc_final: 0.7694 (tp40) REVERT: A 936 CYS cc_start: 0.8492 (m) cc_final: 0.7992 (m) REVERT: A 939 GLU cc_start: 0.7668 (tp30) cc_final: 0.6912 (tp30) REVERT: A 1015 MET cc_start: 0.5380 (mpp) cc_final: 0.4680 (mpp) REVERT: A 1079 TYR cc_start: 0.6756 (m-10) cc_final: 0.6291 (m-10) REVERT: A 1214 LYS cc_start: 0.8344 (mttt) cc_final: 0.7820 (pttm) REVERT: A 1229 VAL cc_start: 0.8166 (t) cc_final: 0.7406 (t) REVERT: A 1233 ASN cc_start: 0.7327 (m110) cc_final: 0.6990 (m-40) REVERT: A 1250 HIS cc_start: 0.6094 (m90) cc_final: 0.5548 (m90) REVERT: A 1294 ASP cc_start: 0.8878 (m-30) cc_final: 0.8579 (m-30) REVERT: A 1320 GLN cc_start: 0.8322 (tp40) cc_final: 0.7991 (tp40) REVERT: A 1324 ASP cc_start: 0.8063 (m-30) cc_final: 0.7352 (m-30) REVERT: A 1339 SER cc_start: 0.9067 (t) cc_final: 0.8852 (p) REVERT: A 1342 LEU cc_start: 0.8479 (tp) cc_final: 0.8224 (tp) REVERT: A 1343 LEU cc_start: 0.8578 (mt) cc_final: 0.8362 (pp) REVERT: A 1346 LEU cc_start: 0.9118 (mt) cc_final: 0.8871 (mt) REVERT: A 1351 ASN cc_start: 0.7780 (t0) cc_final: 0.7434 (t0) REVERT: A 1352 ASN cc_start: 0.7259 (p0) cc_final: 0.7001 (p0) REVERT: A 1357 GLU cc_start: 0.6825 (tm-30) cc_final: 0.6582 (tm-30) REVERT: A 1366 LYS cc_start: 0.9181 (mttt) cc_final: 0.8776 (mttt) REVERT: A 1378 LEU cc_start: 0.7410 (tp) cc_final: 0.6692 (tp) REVERT: A 1403 LEU cc_start: 0.8055 (mt) cc_final: 0.7675 (mp) REVERT: A 1414 LYS cc_start: 0.7956 (tttp) cc_final: 0.7594 (tmtt) REVERT: A 1456 GLU cc_start: 0.7625 (pp20) cc_final: 0.7178 (pp20) REVERT: A 1502 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7536 (tp-100) REVERT: A 1508 LEU cc_start: 0.8904 (tp) cc_final: 0.7227 (tp) REVERT: A 1512 TYR cc_start: 0.7123 (m-80) cc_final: 0.6838 (m-80) REVERT: A 1530 ASP cc_start: 0.6468 (m-30) cc_final: 0.6230 (m-30) REVERT: A 1531 GLN cc_start: 0.8470 (mt0) cc_final: 0.7688 (mm110) REVERT: A 1537 ASN cc_start: 0.8474 (m110) cc_final: 0.8208 (m110) REVERT: A 1546 MET cc_start: 0.8353 (tpp) cc_final: 0.8084 (mmm) REVERT: A 1580 MET cc_start: 0.6390 (mtp) cc_final: 0.5808 (mtp) REVERT: A 1583 CYS cc_start: 0.8261 (p) cc_final: 0.7675 (p) outliers start: 1 outliers final: 0 residues processed: 294 average time/residue: 0.2556 time to fit residues: 104.1287 Evaluate side-chains 265 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 95 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1415 GLN A1490 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.135183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.116293 restraints weight = 33624.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.119442 restraints weight = 21962.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.121669 restraints weight = 15585.537| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6482 moved from start: 0.5942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11310 Z= 0.160 Angle : 0.640 10.954 15262 Z= 0.331 Chirality : 0.042 0.227 1709 Planarity : 0.005 0.071 1973 Dihedral : 5.347 72.411 1510 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.83 (0.23), residues: 1375 helix: 1.29 (0.18), residues: 786 sheet: -0.74 (0.38), residues: 156 loop : -0.14 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 369 HIS 0.006 0.001 HIS A 110 PHE 0.025 0.002 PHE A 291 TYR 0.011 0.002 TYR A 64 ARG 0.009 0.001 ARG A1271 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 691) hydrogen bonds : angle 4.78338 ( 2007) covalent geometry : bond 0.00338 (11310) covalent geometry : angle 0.63987 (15262) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LEU cc_start: 0.7180 (mt) cc_final: 0.6875 (pp) REVERT: A 108 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7864 (pt0) REVERT: A 353 TYR cc_start: 0.7990 (m-80) cc_final: 0.7692 (m-10) REVERT: A 360 LYS cc_start: 0.7965 (pptt) cc_final: 0.7671 (pptt) REVERT: A 419 MET cc_start: 0.7414 (mmp) cc_final: 0.6917 (tpt) REVERT: A 511 MET cc_start: 0.6467 (mmp) cc_final: 0.5966 (mmp) REVERT: A 539 TYR cc_start: 0.7518 (m-80) cc_final: 0.6943 (m-80) REVERT: A 540 LYS cc_start: 0.8430 (mttp) cc_final: 0.7892 (ptpt) REVERT: A 577 MET cc_start: 0.5678 (ttp) cc_final: 0.4963 (ttt) REVERT: A 598 ASP cc_start: 0.7994 (m-30) cc_final: 0.7481 (m-30) REVERT: A 691 SER cc_start: 0.7079 (m) cc_final: 0.6746 (p) REVERT: A 741 MET cc_start: 0.7625 (mtt) cc_final: 0.6982 (mtt) REVERT: A 760 MET cc_start: 0.7925 (ttp) cc_final: 0.7717 (tpp) REVERT: A 792 HIS cc_start: 0.7551 (t-170) cc_final: 0.7293 (t70) REVERT: A 859 TYR cc_start: 0.7680 (p90) cc_final: 0.7336 (p90) REVERT: A 926 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8166 (mttt) REVERT: A 928 GLU cc_start: 0.8481 (tt0) cc_final: 0.8217 (tt0) REVERT: A 932 GLN cc_start: 0.7971 (mt0) cc_final: 0.7605 (tp40) REVERT: A 936 CYS cc_start: 0.8505 (m) cc_final: 0.7977 (m) REVERT: A 939 GLU cc_start: 0.7634 (tp30) cc_final: 0.7296 (tp30) REVERT: A 1079 TYR cc_start: 0.6891 (m-10) cc_final: 0.6395 (m-10) REVERT: A 1214 LYS cc_start: 0.8351 (mttt) cc_final: 0.7880 (pttm) REVERT: A 1229 VAL cc_start: 0.8143 (t) cc_final: 0.7500 (t) REVERT: A 1250 HIS cc_start: 0.6166 (m90) cc_final: 0.5285 (m90) REVERT: A 1320 GLN cc_start: 0.8340 (tp40) cc_final: 0.7927 (tp40) REVERT: A 1323 ARG cc_start: 0.7784 (ttt180) cc_final: 0.7264 (ttt90) REVERT: A 1324 ASP cc_start: 0.8204 (m-30) cc_final: 0.7446 (m-30) REVERT: A 1339 SER cc_start: 0.9164 (t) cc_final: 0.8918 (p) REVERT: A 1342 LEU cc_start: 0.8363 (tp) cc_final: 0.8052 (tp) REVERT: A 1343 LEU cc_start: 0.8594 (mt) cc_final: 0.8344 (pp) REVERT: A 1346 LEU cc_start: 0.9099 (mt) cc_final: 0.8680 (mt) REVERT: A 1357 GLU cc_start: 0.6771 (tm-30) cc_final: 0.6475 (tm-30) REVERT: A 1366 LYS cc_start: 0.9155 (mttt) cc_final: 0.8804 (mttt) REVERT: A 1378 LEU cc_start: 0.7318 (tp) cc_final: 0.6528 (tp) REVERT: A 1403 LEU cc_start: 0.7962 (mt) cc_final: 0.7698 (mp) REVERT: A 1414 LYS cc_start: 0.8022 (tttp) cc_final: 0.7629 (tmtt) REVERT: A 1415 GLN cc_start: 0.7278 (tt0) cc_final: 0.6510 (tt0) REVERT: A 1453 SER cc_start: 0.8611 (p) cc_final: 0.8167 (p) REVERT: A 1456 GLU cc_start: 0.7522 (pp20) cc_final: 0.7307 (pp20) REVERT: A 1502 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7529 (tm-30) REVERT: A 1530 ASP cc_start: 0.6504 (m-30) cc_final: 0.6298 (m-30) REVERT: A 1531 GLN cc_start: 0.8497 (mt0) cc_final: 0.7689 (mm110) REVERT: A 1537 ASN cc_start: 0.8487 (m110) cc_final: 0.8259 (m110) REVERT: A 1580 MET cc_start: 0.6374 (mtp) cc_final: 0.5801 (mtp) REVERT: A 1583 CYS cc_start: 0.8110 (p) cc_final: 0.7485 (p) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2609 time to fit residues: 103.5724 Evaluate side-chains 252 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 133 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 136 optimal weight: 0.0000 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 285 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 ASN ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.134799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.116042 restraints weight = 33696.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.119222 restraints weight = 21787.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.121492 restraints weight = 15368.286| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11310 Z= 0.154 Angle : 0.651 10.197 15262 Z= 0.336 Chirality : 0.042 0.291 1709 Planarity : 0.005 0.054 1973 Dihedral : 5.291 70.341 1510 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.93 (0.23), residues: 1375 helix: 1.41 (0.18), residues: 781 sheet: -0.85 (0.36), residues: 159 loop : -0.09 (0.32), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 787 HIS 0.005 0.001 HIS A 77 PHE 0.017 0.002 PHE A1549 TYR 0.012 0.001 TYR A 300 ARG 0.010 0.001 ARG A1454 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 691) hydrogen bonds : angle 4.72545 ( 2007) covalent geometry : bond 0.00331 (11310) covalent geometry : angle 0.65096 (15262) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7952 (pt0) REVERT: A 202 TYR cc_start: 0.6594 (m-10) cc_final: 0.5931 (m-80) REVERT: A 247 LEU cc_start: 0.6159 (mt) cc_final: 0.5714 (mt) REVERT: A 257 ILE cc_start: 0.7262 (mt) cc_final: 0.7025 (mt) REVERT: A 278 LEU cc_start: 0.7968 (pp) cc_final: 0.7737 (pp) REVERT: A 353 TYR cc_start: 0.8003 (m-80) cc_final: 0.7707 (m-10) REVERT: A 360 LYS cc_start: 0.7867 (pptt) cc_final: 0.7628 (pptt) REVERT: A 539 TYR cc_start: 0.7557 (m-80) cc_final: 0.6931 (m-80) REVERT: A 540 LYS cc_start: 0.8421 (mttp) cc_final: 0.7891 (ptpt) REVERT: A 577 MET cc_start: 0.5497 (ttp) cc_final: 0.4952 (ttt) REVERT: A 598 ASP cc_start: 0.7992 (m-30) cc_final: 0.7481 (m-30) REVERT: A 691 SER cc_start: 0.7052 (m) cc_final: 0.6741 (p) REVERT: A 741 MET cc_start: 0.7593 (mtt) cc_final: 0.7028 (mtt) REVERT: A 792 HIS cc_start: 0.7601 (t-170) cc_final: 0.7267 (t70) REVERT: A 859 TYR cc_start: 0.7643 (p90) cc_final: 0.7285 (p90) REVERT: A 926 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8189 (mttt) REVERT: A 928 GLU cc_start: 0.8522 (tt0) cc_final: 0.8259 (tt0) REVERT: A 932 GLN cc_start: 0.8035 (mt0) cc_final: 0.7636 (tp40) REVERT: A 936 CYS cc_start: 0.8588 (m) cc_final: 0.8058 (m) REVERT: A 939 GLU cc_start: 0.7717 (tp30) cc_final: 0.7357 (tp30) REVERT: A 953 LYS cc_start: 0.7863 (ttpt) cc_final: 0.7611 (ttpt) REVERT: A 1017 TYR cc_start: 0.7041 (m-80) cc_final: 0.6791 (m-10) REVERT: A 1021 CYS cc_start: 0.8148 (t) cc_final: 0.7755 (t) REVERT: A 1022 ILE cc_start: 0.7357 (mp) cc_final: 0.6803 (tt) REVERT: A 1079 TYR cc_start: 0.6918 (m-10) cc_final: 0.6463 (m-10) REVERT: A 1214 LYS cc_start: 0.8350 (mttt) cc_final: 0.7879 (pttm) REVERT: A 1229 VAL cc_start: 0.8108 (t) cc_final: 0.7435 (t) REVERT: A 1250 HIS cc_start: 0.5972 (m90) cc_final: 0.5446 (m90) REVERT: A 1320 GLN cc_start: 0.8403 (tp40) cc_final: 0.7988 (tp40) REVERT: A 1324 ASP cc_start: 0.8286 (m-30) cc_final: 0.7547 (m-30) REVERT: A 1328 CYS cc_start: 0.7919 (m) cc_final: 0.7707 (m) REVERT: A 1339 SER cc_start: 0.9121 (t) cc_final: 0.8912 (p) REVERT: A 1343 LEU cc_start: 0.8565 (mt) cc_final: 0.8280 (pp) REVERT: A 1357 GLU cc_start: 0.6720 (tm-30) cc_final: 0.6135 (tm-30) REVERT: A 1366 LYS cc_start: 0.9142 (mttt) cc_final: 0.8826 (mttt) REVERT: A 1378 LEU cc_start: 0.7571 (tp) cc_final: 0.6969 (tp) REVERT: A 1403 LEU cc_start: 0.7921 (mt) cc_final: 0.7660 (mp) REVERT: A 1414 LYS cc_start: 0.7957 (tttp) cc_final: 0.7421 (tmtt) REVERT: A 1415 GLN cc_start: 0.7203 (tt0) cc_final: 0.6435 (tt0) REVERT: A 1463 LEU cc_start: 0.8173 (tp) cc_final: 0.7860 (tp) REVERT: A 1488 ASP cc_start: 0.7643 (m-30) cc_final: 0.7433 (m-30) REVERT: A 1502 GLN cc_start: 0.8189 (tm-30) cc_final: 0.7619 (tm-30) REVERT: A 1512 TYR cc_start: 0.7368 (m-80) cc_final: 0.7080 (m-80) REVERT: A 1514 GLU cc_start: 0.7929 (mp0) cc_final: 0.7275 (mp0) REVERT: A 1530 ASP cc_start: 0.6575 (m-30) cc_final: 0.6326 (m-30) REVERT: A 1531 GLN cc_start: 0.8495 (mt0) cc_final: 0.7746 (mm110) REVERT: A 1537 ASN cc_start: 0.8530 (m110) cc_final: 0.8299 (m110) REVERT: A 1546 MET cc_start: 0.8712 (mtt) cc_final: 0.8400 (mtt) REVERT: A 1580 MET cc_start: 0.6616 (mtp) cc_final: 0.5829 (mtp) REVERT: A 1583 CYS cc_start: 0.7997 (p) cc_final: 0.7696 (p) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2572 time to fit residues: 101.2773 Evaluate side-chains 249 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 3 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 135 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN A1070 GLN A1101 ASN ** A1250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1435 GLN A1502 GLN A1503 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.136685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.118081 restraints weight = 33243.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.121262 restraints weight = 21541.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.123496 restraints weight = 15249.969| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6450 moved from start: 0.6455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11310 Z= 0.139 Angle : 0.644 10.263 15262 Z= 0.330 Chirality : 0.042 0.298 1709 Planarity : 0.005 0.089 1973 Dihedral : 5.259 67.717 1510 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.86 (0.23), residues: 1375 helix: 1.34 (0.19), residues: 781 sheet: -0.91 (0.37), residues: 153 loop : -0.10 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 787 HIS 0.005 0.001 HIS A 578 PHE 0.019 0.002 PHE A 370 TYR 0.027 0.001 TYR A 937 ARG 0.012 0.001 ARG A1271 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 691) hydrogen bonds : angle 4.71124 ( 2007) covalent geometry : bond 0.00305 (11310) covalent geometry : angle 0.64426 (15262) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8450 (mm-30) cc_final: 0.7992 (pt0) REVERT: A 202 TYR cc_start: 0.6549 (m-10) cc_final: 0.5929 (m-80) REVERT: A 257 ILE cc_start: 0.7332 (mt) cc_final: 0.7107 (mt) REVERT: A 264 ASN cc_start: 0.7609 (t0) cc_final: 0.7348 (t0) REVERT: A 278 LEU cc_start: 0.8197 (pp) cc_final: 0.7914 (pp) REVERT: A 353 TYR cc_start: 0.7996 (m-80) cc_final: 0.7663 (m-10) REVERT: A 519 CYS cc_start: 0.8968 (m) cc_final: 0.8765 (m) REVERT: A 539 TYR cc_start: 0.7507 (m-80) cc_final: 0.6901 (m-80) REVERT: A 540 LYS cc_start: 0.8423 (mttp) cc_final: 0.7865 (ptpt) REVERT: A 577 MET cc_start: 0.5452 (ttp) cc_final: 0.4946 (ttt) REVERT: A 598 ASP cc_start: 0.7927 (m-30) cc_final: 0.7403 (m-30) REVERT: A 691 SER cc_start: 0.6963 (m) cc_final: 0.6641 (p) REVERT: A 741 MET cc_start: 0.7530 (mtt) cc_final: 0.6822 (mtt) REVERT: A 859 TYR cc_start: 0.7642 (p90) cc_final: 0.7329 (p90) REVERT: A 926 LYS cc_start: 0.8576 (mtmm) cc_final: 0.8175 (mttt) REVERT: A 928 GLU cc_start: 0.8449 (tt0) cc_final: 0.8228 (tt0) REVERT: A 932 GLN cc_start: 0.8109 (mt0) cc_final: 0.7874 (tp40) REVERT: A 936 CYS cc_start: 0.8537 (m) cc_final: 0.7920 (m) REVERT: A 937 TYR cc_start: 0.8312 (m-80) cc_final: 0.8110 (m-80) REVERT: A 939 GLU cc_start: 0.7694 (tp30) cc_final: 0.7320 (tp30) REVERT: A 953 LYS cc_start: 0.7813 (ttpt) cc_final: 0.7573 (ttpt) REVERT: A 1022 ILE cc_start: 0.7364 (mp) cc_final: 0.6648 (mp) REVERT: A 1079 TYR cc_start: 0.6909 (m-10) cc_final: 0.6309 (m-10) REVERT: A 1214 LYS cc_start: 0.8318 (mttt) cc_final: 0.7848 (pttm) REVERT: A 1229 VAL cc_start: 0.8074 (t) cc_final: 0.7603 (t) REVERT: A 1236 LEU cc_start: 0.8784 (mm) cc_final: 0.8564 (mm) REVERT: A 1250 HIS cc_start: 0.5800 (m90) cc_final: 0.5403 (m90) REVERT: A 1320 GLN cc_start: 0.8377 (tp40) cc_final: 0.7687 (tp40) REVERT: A 1324 ASP cc_start: 0.8227 (m-30) cc_final: 0.7353 (m-30) REVERT: A 1328 CYS cc_start: 0.7896 (m) cc_final: 0.7590 (m) REVERT: A 1339 SER cc_start: 0.9108 (t) cc_final: 0.8800 (p) REVERT: A 1343 LEU cc_start: 0.8541 (mt) cc_final: 0.8232 (pp) REVERT: A 1357 GLU cc_start: 0.6884 (tm-30) cc_final: 0.6371 (tm-30) REVERT: A 1382 SER cc_start: 0.7888 (t) cc_final: 0.7630 (t) REVERT: A 1384 LEU cc_start: 0.8416 (mt) cc_final: 0.8081 (mt) REVERT: A 1403 LEU cc_start: 0.7883 (mt) cc_final: 0.7656 (mp) REVERT: A 1414 LYS cc_start: 0.8027 (tttp) cc_final: 0.7482 (tmtt) REVERT: A 1415 GLN cc_start: 0.7160 (tt0) cc_final: 0.6350 (tt0) REVERT: A 1453 SER cc_start: 0.8733 (p) cc_final: 0.8270 (p) REVERT: A 1456 GLU cc_start: 0.7633 (pp20) cc_final: 0.7410 (pp20) REVERT: A 1474 ASN cc_start: 0.7628 (p0) cc_final: 0.7401 (p0) REVERT: A 1488 ASP cc_start: 0.7551 (m-30) cc_final: 0.7310 (m-30) REVERT: A 1502 GLN cc_start: 0.8164 (tm130) cc_final: 0.7587 (tm-30) REVERT: A 1514 GLU cc_start: 0.7980 (mp0) cc_final: 0.7287 (mp0) REVERT: A 1530 ASP cc_start: 0.6555 (m-30) cc_final: 0.6335 (m-30) REVERT: A 1531 GLN cc_start: 0.8472 (mt0) cc_final: 0.7707 (mm110) REVERT: A 1537 ASN cc_start: 0.8537 (m110) cc_final: 0.8280 (m110) REVERT: A 1541 GLU cc_start: 0.8098 (tp30) cc_final: 0.7844 (tp30) REVERT: A 1546 MET cc_start: 0.8665 (mtt) cc_final: 0.8366 (mtt) REVERT: A 1570 GLU cc_start: 0.7590 (mp0) cc_final: 0.7373 (mp0) REVERT: A 1580 MET cc_start: 0.6647 (mtp) cc_final: 0.6066 (mtp) REVERT: A 1583 CYS cc_start: 0.8251 (p) cc_final: 0.7837 (p) REVERT: A 1632 LYS cc_start: 0.7856 (mptt) cc_final: 0.7535 (mmtm) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.2522 time to fit residues: 100.5765 Evaluate side-chains 256 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 10 optimal weight: 6.9990 chunk 104 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 128 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 36 optimal weight: 0.0000 chunk 78 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN ** A1370 GLN ** 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 = 0.4219 r_free = 0.4219 target = 0.136971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.118271 restraints weight = 32856.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.121482 restraints weight = 21518.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.123734 restraints weight = 15268.979| |-----------------------------------------------------------------------------| r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11310 Z= 0.139 Angle : 0.669 10.375 15262 Z= 0.341 Chirality : 0.043 0.280 1709 Planarity : 0.004 0.076 1973 Dihedral : 5.121 63.978 1510 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.98 (0.23), residues: 1375 helix: 1.42 (0.19), residues: 780 sheet: -0.78 (0.38), residues: 150 loop : -0.06 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP A 369 HIS 0.004 0.001 HIS A 578 PHE 0.014 0.001 PHE A1338 TYR 0.020 0.001 TYR A 937 ARG 0.011 0.001 ARG A1073 Details of bonding type rmsd hydrogen bonds : bond 0.04127 ( 691) hydrogen bonds : angle 4.72892 ( 2007) covalent geometry : bond 0.00308 (11310) covalent geometry : angle 0.66930 (15262) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7995 (pt0) REVERT: A 202 TYR cc_start: 0.6597 (m-10) cc_final: 0.6174 (m-80) REVERT: A 264 ASN cc_start: 0.7580 (t0) cc_final: 0.7184 (t0) REVERT: A 278 LEU cc_start: 0.8273 (pp) cc_final: 0.7900 (pp) REVERT: A 353 TYR cc_start: 0.7963 (m-80) cc_final: 0.7631 (m-10) REVERT: A 356 THR cc_start: 0.8422 (p) cc_final: 0.8168 (t) REVERT: A 419 MET cc_start: 0.7875 (mmp) cc_final: 0.7493 (tpt) REVERT: A 539 TYR cc_start: 0.7480 (m-80) cc_final: 0.6941 (m-80) REVERT: A 540 LYS cc_start: 0.8400 (mttp) cc_final: 0.7828 (ptpt) REVERT: A 577 MET cc_start: 0.5654 (ttp) cc_final: 0.5027 (ttt) REVERT: A 598 ASP cc_start: 0.8125 (m-30) cc_final: 0.7468 (m-30) REVERT: A 679 ARG cc_start: 0.7322 (mtp-110) cc_final: 0.6894 (mtp-110) REVERT: A 691 SER cc_start: 0.6925 (m) cc_final: 0.6636 (p) REVERT: A 722 GLN cc_start: 0.6856 (mt0) cc_final: 0.6609 (mt0) REVERT: A 741 MET cc_start: 0.7509 (mtt) cc_final: 0.6828 (mtt) REVERT: A 859 TYR cc_start: 0.7687 (p90) cc_final: 0.7393 (p90) REVERT: A 926 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8193 (mttt) REVERT: A 928 GLU cc_start: 0.8413 (tt0) cc_final: 0.8162 (tt0) REVERT: A 932 GLN cc_start: 0.8130 (mt0) cc_final: 0.7884 (tp40) REVERT: A 933 ARG cc_start: 0.8669 (ttm170) cc_final: 0.7966 (ttm170) REVERT: A 936 CYS cc_start: 0.8626 (m) cc_final: 0.7977 (m) REVERT: A 937 TYR cc_start: 0.8347 (m-80) cc_final: 0.8116 (m-80) REVERT: A 953 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7496 (ttpt) REVERT: A 1021 CYS cc_start: 0.7731 (t) cc_final: 0.7216 (t) REVERT: A 1022 ILE cc_start: 0.7431 (mp) cc_final: 0.7170 (tt) REVERT: A 1079 TYR cc_start: 0.6925 (m-10) cc_final: 0.6359 (m-10) REVERT: A 1214 LYS cc_start: 0.8322 (mttt) cc_final: 0.7845 (pttm) REVERT: A 1229 VAL cc_start: 0.8013 (t) cc_final: 0.7521 (t) REVERT: A 1250 HIS cc_start: 0.5814 (m90) cc_final: 0.5410 (m90) REVERT: A 1283 TRP cc_start: 0.6946 (m100) cc_final: 0.6300 (m-90) REVERT: A 1294 ASP cc_start: 0.8782 (m-30) cc_final: 0.8545 (m-30) REVERT: A 1319 LEU cc_start: 0.7671 (mt) cc_final: 0.7443 (tt) REVERT: A 1320 GLN cc_start: 0.8338 (tp40) cc_final: 0.7832 (tm-30) REVERT: A 1323 ARG cc_start: 0.7677 (ttt180) cc_final: 0.7451 (mtt-85) REVERT: A 1324 ASP cc_start: 0.8301 (m-30) cc_final: 0.7341 (m-30) REVERT: A 1328 CYS cc_start: 0.7995 (m) cc_final: 0.7706 (m) REVERT: A 1357 GLU cc_start: 0.6897 (tm-30) cc_final: 0.6378 (tm-30) REVERT: A 1382 SER cc_start: 0.7735 (t) cc_final: 0.7526 (t) REVERT: A 1403 LEU cc_start: 0.7694 (mt) cc_final: 0.7469 (mp) REVERT: A 1414 LYS cc_start: 0.7959 (tttp) cc_final: 0.7417 (tmtt) REVERT: A 1415 GLN cc_start: 0.7105 (tt0) cc_final: 0.6292 (tt0) REVERT: A 1470 LYS cc_start: 0.8079 (pttp) cc_final: 0.7845 (pttp) REVERT: A 1474 ASN cc_start: 0.7617 (p0) cc_final: 0.7359 (p0) REVERT: A 1488 ASP cc_start: 0.7682 (m-30) cc_final: 0.7458 (m-30) REVERT: A 1512 TYR cc_start: 0.7401 (m-80) cc_final: 0.7090 (m-80) REVERT: A 1530 ASP cc_start: 0.6681 (m-30) cc_final: 0.6456 (m-30) REVERT: A 1531 GLN cc_start: 0.8344 (mt0) cc_final: 0.7643 (mm110) REVERT: A 1537 ASN cc_start: 0.8526 (m110) cc_final: 0.8292 (m110) REVERT: A 1541 GLU cc_start: 0.8015 (tp30) cc_final: 0.7770 (tp30) REVERT: A 1546 MET cc_start: 0.8661 (mtt) cc_final: 0.8307 (mtt) REVERT: A 1580 MET cc_start: 0.6680 (mtp) cc_final: 0.6218 (mtp) outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.2554 time to fit residues: 102.6328 Evaluate side-chains 257 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 97 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 GLN ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1095 GLN ** A1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1435 GLN A1502 GLN ** A1598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.136673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.117913 restraints weight = 33441.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.121109 restraints weight = 21939.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.123411 restraints weight = 15558.730| |-----------------------------------------------------------------------------| r_work (final): 0.3993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.6804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11310 Z= 0.134 Angle : 0.651 9.604 15262 Z= 0.332 Chirality : 0.042 0.273 1709 Planarity : 0.004 0.070 1973 Dihedral : 5.021 60.077 1510 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 1.00 (0.23), residues: 1375 helix: 1.45 (0.18), residues: 778 sheet: -0.64 (0.38), residues: 151 loop : -0.12 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 787 HIS 0.005 0.001 HIS A 578 PHE 0.018 0.002 PHE A1260 TYR 0.013 0.001 TYR A 937 ARG 0.009 0.001 ARG A1271 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 691) hydrogen bonds : angle 4.69850 ( 2007) covalent geometry : bond 0.00296 (11310) covalent geometry : angle 0.65107 (15262) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8020 (pt0) REVERT: A 202 TYR cc_start: 0.6581 (m-10) cc_final: 0.6099 (m-80) REVERT: A 257 ILE cc_start: 0.7261 (mt) cc_final: 0.7010 (mt) REVERT: A 264 ASN cc_start: 0.7647 (t0) cc_final: 0.7230 (t0) REVERT: A 278 LEU cc_start: 0.8281 (pp) cc_final: 0.7819 (pp) REVERT: A 353 TYR cc_start: 0.7886 (m-80) cc_final: 0.7629 (m-10) REVERT: A 356 THR cc_start: 0.8421 (p) cc_final: 0.8209 (t) REVERT: A 359 TRP cc_start: 0.5646 (p90) cc_final: 0.5095 (p90) REVERT: A 373 MET cc_start: 0.6896 (mmp) cc_final: 0.6679 (mmp) REVERT: A 387 ILE cc_start: 0.7446 (mt) cc_final: 0.7064 (mt) REVERT: A 419 MET cc_start: 0.7878 (mmp) cc_final: 0.7488 (tpt) REVERT: A 539 TYR cc_start: 0.7448 (m-80) cc_final: 0.6940 (m-80) REVERT: A 540 LYS cc_start: 0.8356 (mttp) cc_final: 0.7822 (ptpt) REVERT: A 577 MET cc_start: 0.5746 (ttp) cc_final: 0.5100 (ttt) REVERT: A 598 ASP cc_start: 0.8117 (m-30) cc_final: 0.7465 (m-30) REVERT: A 679 ARG cc_start: 0.7179 (mtp-110) cc_final: 0.6976 (mtp-110) REVERT: A 691 SER cc_start: 0.6996 (m) cc_final: 0.6724 (p) REVERT: A 741 MET cc_start: 0.7456 (mtt) cc_final: 0.6770 (mtt) REVERT: A 859 TYR cc_start: 0.7812 (p90) cc_final: 0.7561 (p90) REVERT: A 926 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8115 (mttt) REVERT: A 928 GLU cc_start: 0.8425 (tt0) cc_final: 0.8163 (tt0) REVERT: A 932 GLN cc_start: 0.8164 (mt0) cc_final: 0.7943 (tp40) REVERT: A 933 ARG cc_start: 0.8698 (ttm170) cc_final: 0.8065 (ttm170) REVERT: A 936 CYS cc_start: 0.8722 (m) cc_final: 0.8136 (m) REVERT: A 937 TYR cc_start: 0.8511 (m-80) cc_final: 0.8267 (m-80) REVERT: A 953 LYS cc_start: 0.7781 (ttpt) cc_final: 0.7489 (ttpt) REVERT: A 1079 TYR cc_start: 0.6961 (m-10) cc_final: 0.6305 (m-10) REVERT: A 1214 LYS cc_start: 0.8315 (mttt) cc_final: 0.7805 (pttm) REVERT: A 1229 VAL cc_start: 0.8007 (t) cc_final: 0.7551 (t) REVERT: A 1230 ASP cc_start: 0.7874 (m-30) cc_final: 0.7642 (m-30) REVERT: A 1250 HIS cc_start: 0.6051 (m90) cc_final: 0.5648 (m90) REVERT: A 1283 TRP cc_start: 0.6928 (m100) cc_final: 0.6263 (m-90) REVERT: A 1294 ASP cc_start: 0.8798 (m-30) cc_final: 0.8556 (m-30) REVERT: A 1319 LEU cc_start: 0.7667 (mt) cc_final: 0.7455 (tt) REVERT: A 1320 GLN cc_start: 0.8363 (tp40) cc_final: 0.7814 (tm-30) REVERT: A 1323 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7369 (mtt-85) REVERT: A 1324 ASP cc_start: 0.8367 (m-30) cc_final: 0.7381 (m-30) REVERT: A 1343 LEU cc_start: 0.8587 (mm) cc_final: 0.8082 (pp) REVERT: A 1357 GLU cc_start: 0.6822 (tm-30) cc_final: 0.6262 (tm-30) REVERT: A 1366 LYS cc_start: 0.9106 (mttt) cc_final: 0.8280 (mttt) REVERT: A 1369 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7286 (mp0) REVERT: A 1403 LEU cc_start: 0.7652 (mt) cc_final: 0.7406 (mp) REVERT: A 1414 LYS cc_start: 0.7969 (tttp) cc_final: 0.7451 (tmtt) REVERT: A 1415 GLN cc_start: 0.7141 (tt0) cc_final: 0.6281 (tt0) REVERT: A 1453 SER cc_start: 0.8822 (p) cc_final: 0.8424 (p) REVERT: A 1470 LYS cc_start: 0.8085 (pttp) cc_final: 0.7765 (pttp) REVERT: A 1488 ASP cc_start: 0.7571 (m-30) cc_final: 0.7352 (m-30) REVERT: A 1530 ASP cc_start: 0.6679 (m-30) cc_final: 0.6463 (m-30) REVERT: A 1531 GLN cc_start: 0.8324 (mt0) cc_final: 0.7595 (mm110) REVERT: A 1537 ASN cc_start: 0.8500 (m110) cc_final: 0.8260 (m110) REVERT: A 1541 GLU cc_start: 0.7993 (tp30) cc_final: 0.7767 (tp30) REVERT: A 1546 MET cc_start: 0.8624 (mtt) cc_final: 0.8290 (mtt) REVERT: A 1580 MET cc_start: 0.6604 (mtp) cc_final: 0.6247 (mtp) REVERT: A 1587 MET cc_start: 0.2200 (mmm) cc_final: 0.1013 (mmm) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.2611 time to fit residues: 102.7719 Evaluate side-chains 257 residues out of total 1223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 32 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 134 optimal weight: 0.3980 chunk 114 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1598 GLN ** 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 = 0.4223 r_free = 0.4223 target = 0.137007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.118302 restraints weight = 33213.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.121441 restraints weight = 21900.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.123694 restraints weight = 15629.143| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6439 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11310 Z= 0.134 Angle : 0.667 9.917 15262 Z= 0.341 Chirality : 0.043 0.273 1709 Planarity : 0.005 0.116 1973 Dihedral : 5.007 55.208 1510 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.00 % 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: 0.98 (0.23), residues: 1375 helix: 1.41 (0.19), residues: 783 sheet: -0.48 (0.39), residues: 151 loop : -0.16 (0.32), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 787 HIS 0.004 0.001 HIS A 916 PHE 0.024 0.002 PHE A 721 TYR 0.018 0.001 TYR A 937 ARG 0.015 0.001 ARG A1454 Details of bonding type rmsd hydrogen bonds : bond 0.04076 ( 691) hydrogen bonds : angle 4.71147 ( 2007) covalent geometry : bond 0.00294 (11310) covalent geometry : angle 0.66708 (15262) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4298.57 seconds wall clock time: 76 minutes 35.92 seconds (4595.92 seconds total)