Starting phenix.real_space_refine on Tue Jun 10 03:37:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vx9_43613/06_2025/8vx9_43613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vx9_43613/06_2025/8vx9_43613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vx9_43613/06_2025/8vx9_43613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vx9_43613/06_2025/8vx9_43613.map" model { file = "/net/cci-nas-00/data/ceres_data/8vx9_43613/06_2025/8vx9_43613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vx9_43613/06_2025/8vx9_43613.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 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 39 5.16 5 C 7076 2.51 5 N 2004 2.21 5 O 2125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 11244 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2028 Classifications: {'peptide': 259} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "B" Number of atoms: 9216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9216 Classifications: {'peptide': 1174} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1123} Time building chain proxies: 6.88, per 1000 atoms: 0.61 Number of scatterers: 11244 At special positions: 0 Unit cell: (93.272, 96.416, 147.768, 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 39 16.00 O 2125 8.00 N 2004 7.00 C 7076 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: 2.73 Conformation dependent library (CDL) restraints added in 2.0 seconds 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2666 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 7 sheets defined 57.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 removed outlier: 3.887A pdb=" N ASP A 6 " --> pdb=" O ASN A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 3 through 6' Processing helix chain 'A' and resid 29 through 40 removed outlier: 4.149A pdb=" N GLY A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 58 Processing helix chain 'A' and resid 60 through 69 Processing helix chain 'A' and resid 76 through 95 removed outlier: 3.817A pdb=" N GLY A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLY A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLU A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 165 through 180 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 198 through 200 No H-bonds generated for 'chain 'A' and resid 198 through 200' Processing helix chain 'A' and resid 214 through 224 Processing helix chain 'A' and resid 240 through 247 Processing helix chain 'A' and resid 248 through 259 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 50 through 72 Processing helix chain 'B' and resid 76 through 95 Processing helix chain 'B' and resid 103 through 118 Processing helix chain 'B' and resid 120 through 129 Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 151 through 166 Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'B' and resid 192 through 224 Processing helix chain 'B' and resid 225 through 246 removed outlier: 3.924A pdb=" N LEU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 267 removed outlier: 3.566A pdb=" N SER B 267 " --> pdb=" O SER B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 285 through 299 Processing helix chain 'B' and resid 308 through 310 No H-bonds generated for 'chain 'B' and resid 308 through 310' Processing helix chain 'B' and resid 311 through 318 Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.876A pdb=" N ILE B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 349 " --> pdb=" O ARG B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 375 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 407 through 418 Processing helix chain 'B' and resid 419 through 423 removed outlier: 3.688A pdb=" N ILE B 422 " --> pdb=" O PRO B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 454 Processing helix chain 'B' and resid 457 through 461 removed outlier: 3.521A pdb=" N ARG B 461 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 485 removed outlier: 3.631A pdb=" N LEU B 476 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE B 479 " --> pdb=" O GLN B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 578 through 583 removed outlier: 3.894A pdb=" N VAL B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 583' Processing helix chain 'B' and resid 583 through 595 removed outlier: 4.270A pdb=" N GLU B 587 " --> pdb=" O GLU B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 608 Processing helix chain 'B' and resid 609 through 618 removed outlier: 3.872A pdb=" N GLU B 618 " --> pdb=" O SER B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 631 Processing helix chain 'B' and resid 642 through 655 removed outlier: 3.540A pdb=" N ARG B 646 " --> pdb=" O PRO B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 670 Processing helix chain 'B' and resid 691 through 701 removed outlier: 3.540A pdb=" N ARG B 701 " --> pdb=" O ASN B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 734 Processing helix chain 'B' and resid 742 through 760 Processing helix chain 'B' and resid 762 through 773 Processing helix chain 'B' and resid 786 through 813 Processing helix chain 'B' and resid 821 through 830 Processing helix chain 'B' and resid 833 through 842 removed outlier: 3.590A pdb=" N ARG B 841 " --> pdb=" O ARG B 837 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 842 " --> pdb=" O SER B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 866 removed outlier: 3.534A pdb=" N ARG B 848 " --> pdb=" O ASP B 844 " (cutoff:3.500A) Processing helix chain 'B' and resid 867 through 878 Processing helix chain 'B' and resid 881 through 889 Processing helix chain 'B' and resid 890 through 904 Processing helix chain 'B' and resid 912 through 923 Processing helix chain 'B' and resid 938 through 948 removed outlier: 4.253A pdb=" N ILE B 942 " --> pdb=" O ASP B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 969 removed outlier: 3.707A pdb=" N GLU B 962 " --> pdb=" O THR B 958 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 966 " --> pdb=" O GLU B 962 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL B 967 " --> pdb=" O THR B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 989 Processing helix chain 'B' and resid 1006 through 1011 Processing helix chain 'B' and resid 1020 through 1028 removed outlier: 3.503A pdb=" N GLY B1028 " --> pdb=" O LEU B1024 " (cutoff:3.500A) Processing helix chain 'B' and resid 1031 through 1043 removed outlier: 3.645A pdb=" N ILE B1036 " --> pdb=" O ARG B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1048 through 1056 Processing helix chain 'B' and resid 1059 through 1065 Processing helix chain 'B' and resid 1078 through 1085 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 7.358A pdb=" N GLN A 21 " --> pdb=" O CYS A 235 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ARG A 237 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 23 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 125 Processing sheet with id=AA3, first strand: chain 'B' and resid 381 through 383 removed outlier: 6.822A pdb=" N SER B 382 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N ARG B 352 " --> pdb=" O VAL B 425 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU B 427 " --> pdb=" O ARG B 352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 522 through 531 removed outlier: 4.725A pdb=" N ALA B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL B 519 " --> pdb=" O ALA B 523 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N TRP B 525 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU B 517 " --> pdb=" O TRP B 525 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N SER B 527 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU B 515 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLY B 513 " --> pdb=" O PHE B 529 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 518 " --> pdb=" O PHE B 503 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N PHE B 503 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG B 500 " --> pdb=" O GLY B 711 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL B 713 " --> pdb=" O ARG B 500 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLN B 502 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR B 715 " --> pdb=" O GLN B 502 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY B 504 " --> pdb=" O TYR B 715 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE B 717 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N VAL B 506 " --> pdb=" O ILE B 717 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N ILE B 678 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 575 " --> pdb=" O VAL B 679 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 684 through 685 Processing sheet with id=AA6, first strand: chain 'B' and resid 1095 through 1096 Processing sheet with id=AA7, first strand: chain 'B' and resid 1095 through 1096 removed outlier: 8.150A pdb=" N LEU B1150 " --> pdb=" O LEU B1118 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU B1118 " --> pdb=" O LEU B1150 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL B1152 " --> pdb=" O LEU B1116 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR B1119 " --> pdb=" O HIS B1126 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS B1125 " --> pdb=" O ILE B1138 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL B1127 " --> pdb=" O GLY B1136 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY B1136 " --> pdb=" O VAL B1127 " (cutoff:3.500A) 607 hydrogen bonds defined for protein. 1776 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: 4.36 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3841 1.34 - 1.46: 1698 1.46 - 1.57: 5854 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 11459 Sorted by residual: bond pdb=" C TRP B1070 " pdb=" N PRO B1071 " ideal model delta sigma weight residual 1.331 1.349 -0.017 1.20e-02 6.94e+03 2.12e+00 bond pdb=" C LEU B 975 " pdb=" O LEU B 975 " ideal model delta sigma weight residual 1.244 1.229 0.014 1.00e-02 1.00e+04 2.04e+00 bond pdb=" CG1 ILE B1025 " pdb=" CD1 ILE B1025 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.58e+00 bond pdb=" CA TYR B 973 " pdb=" C TYR B 973 " ideal model delta sigma weight residual 1.526 1.510 0.016 1.29e-02 6.01e+03 1.49e+00 bond pdb=" CA TRP B 977 " pdb=" C TRP B 977 " ideal model delta sigma weight residual 1.524 1.509 0.015 1.27e-02 6.20e+03 1.39e+00 ... (remaining 11454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 15113 1.65 - 3.30: 352 3.30 - 4.95: 67 4.95 - 6.60: 11 6.60 - 8.25: 3 Bond angle restraints: 15546 Sorted by residual: angle pdb=" N TYR B 973 " pdb=" CA TYR B 973 " pdb=" C TYR B 973 " ideal model delta sigma weight residual 111.54 104.95 6.59 1.36e+00 5.41e-01 2.34e+01 angle pdb=" CA LEU B 975 " pdb=" C LEU B 975 " pdb=" N PRO B 976 " ideal model delta sigma weight residual 120.77 117.27 3.50 9.70e-01 1.06e+00 1.30e+01 angle pdb=" N TRP B 977 " pdb=" CA TRP B 977 " pdb=" C TRP B 977 " ideal model delta sigma weight residual 111.07 107.35 3.72 1.07e+00 8.73e-01 1.21e+01 angle pdb=" N PHE B 966 " pdb=" CA PHE B 966 " pdb=" C PHE B 966 " ideal model delta sigma weight residual 113.20 109.04 4.16 1.21e+00 6.83e-01 1.18e+01 angle pdb=" N ASN B 969 " pdb=" CA ASN B 969 " pdb=" C ASN B 969 " ideal model delta sigma weight residual 114.64 109.90 4.74 1.52e+00 4.33e-01 9.71e+00 ... (remaining 15541 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6283 17.78 - 35.57: 530 35.57 - 53.35: 76 53.35 - 71.14: 16 71.14 - 88.92: 12 Dihedral angle restraints: 6917 sinusoidal: 2790 harmonic: 4127 Sorted by residual: dihedral pdb=" CA ASP B 324 " pdb=" C ASP B 324 " pdb=" N LEU B 325 " pdb=" CA LEU B 325 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA PHE B 930 " pdb=" C PHE B 930 " pdb=" N ILE B 931 " pdb=" CA ILE B 931 " ideal model delta harmonic sigma weight residual -180.00 -162.02 -17.98 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ARG A 240 " pdb=" C ARG A 240 " pdb=" N HIS A 241 " pdb=" CA HIS A 241 " ideal model delta harmonic sigma weight residual -180.00 -163.10 -16.90 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 6914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1068 0.031 - 0.062: 433 0.062 - 0.094: 173 0.094 - 0.125: 71 0.125 - 0.156: 7 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CG LEU B 229 " pdb=" CB LEU B 229 " pdb=" CD1 LEU B 229 " pdb=" CD2 LEU B 229 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.09e-01 chirality pdb=" CA PRO B 642 " pdb=" N PRO B 642 " pdb=" C PRO B 642 " pdb=" CB PRO B 642 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA VAL B 967 " pdb=" N VAL B 967 " pdb=" C VAL B 967 " pdb=" CB VAL B 967 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 1749 not shown) Planarity restraints: 2032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 256 " 0.015 2.00e-02 2.50e+03 1.52e-02 4.02e+00 pdb=" CG PHE B 256 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE B 256 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 256 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 256 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 256 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 256 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 375 " -0.032 5.00e-02 4.00e+02 4.78e-02 3.66e+00 pdb=" N PRO B 376 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO B 376 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 376 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 641 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO B 642 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " 0.026 5.00e-02 4.00e+02 ... (remaining 2029 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1768 2.76 - 3.29: 11710 3.29 - 3.83: 20141 3.83 - 4.36: 24122 4.36 - 4.90: 40029 Nonbonded interactions: 97770 Sorted by model distance: nonbonded pdb=" OE2 GLU B1060 " pdb=" NE2 HIS B1064 " model vdw 2.221 3.120 nonbonded pdb=" O GLY B 389 " pdb=" NZ LYS B 410 " model vdw 2.226 3.120 nonbonded pdb=" O THR A 100 " pdb=" NZ LYS A 103 " model vdw 2.240 3.120 nonbonded pdb=" OD1 ASP B 591 " pdb=" NH1 ARG B 595 " model vdw 2.254 3.120 nonbonded pdb=" NZ LYS A 108 " pdb=" OD2 ASP B 200 " model vdw 2.285 3.120 ... (remaining 97765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 28.890 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:13.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11459 Z= 0.175 Angle : 0.625 8.250 15546 Z= 0.344 Chirality : 0.042 0.156 1752 Planarity : 0.005 0.048 2032 Dihedral : 13.765 88.924 4251 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.08 % Allowed : 0.08 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.43 (0.22), residues: 1429 helix: 0.62 (0.19), residues: 756 sheet: -0.90 (0.48), residues: 125 loop : -1.36 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 563 HIS 0.007 0.001 HIS B 260 PHE 0.035 0.002 PHE B 256 TYR 0.017 0.002 TYR B 58 ARG 0.002 0.000 ARG A 175 Details of bonding type rmsd hydrogen bonds : bond 0.15086 ( 605) hydrogen bonds : angle 6.55370 ( 1776) covalent geometry : bond 0.00380 (11459) covalent geometry : angle 0.62491 (15546) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1215 (tpp) cc_final: 0.0976 (tpp) REVERT: A 19 TYR cc_start: 0.7481 (t80) cc_final: 0.6363 (t80) REVERT: A 125 ILE cc_start: 0.8230 (mt) cc_final: 0.8012 (mt) REVERT: A 179 GLN cc_start: 0.6997 (mt0) cc_final: 0.6743 (mm-40) REVERT: B 76 ASP cc_start: 0.6579 (m-30) cc_final: 0.5886 (m-30) REVERT: B 130 MET cc_start: 0.8339 (mtp) cc_final: 0.8134 (mtm) REVERT: B 525 TRP cc_start: 0.7554 (p90) cc_final: 0.7341 (p90) REVERT: B 602 PHE cc_start: 0.8145 (t80) cc_final: 0.7879 (t80) REVERT: B 715 TYR cc_start: 0.7976 (t80) cc_final: 0.7743 (t80) REVERT: B 852 LYS cc_start: 0.7142 (tttt) cc_final: 0.6895 (tttt) REVERT: B 977 TRP cc_start: 0.4842 (t60) cc_final: 0.4572 (t-100) outliers start: 1 outliers final: 2 residues processed: 259 average time/residue: 1.3590 time to fit residues: 380.9490 Evaluate side-chains 228 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 796 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.0980 chunk 72 optimal weight: 0.0970 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 43 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN ** B 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.185034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170630 restraints weight = 15123.558| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 1.71 r_work: 0.4152 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.4024 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11459 Z= 0.159 Angle : 0.619 10.437 15546 Z= 0.318 Chirality : 0.044 0.165 1752 Planarity : 0.005 0.062 2032 Dihedral : 5.340 82.098 1582 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.18 % Allowed : 9.80 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.32 (0.22), residues: 1429 helix: 0.77 (0.19), residues: 766 sheet: -1.24 (0.42), residues: 149 loop : -1.32 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 977 HIS 0.006 0.001 HIS B 260 PHE 0.022 0.002 PHE B1046 TYR 0.020 0.002 TYR B 874 ARG 0.005 0.000 ARG B1151 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 605) hydrogen bonds : angle 5.11817 ( 1776) covalent geometry : bond 0.00361 (11459) covalent geometry : angle 0.61935 (15546) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1247 (tpp) cc_final: 0.1009 (tpp) REVERT: A 140 LYS cc_start: 0.7920 (OUTLIER) cc_final: 0.7682 (mmmt) REVERT: A 179 GLN cc_start: 0.7221 (mt0) cc_final: 0.6941 (mm-40) REVERT: A 182 GLU cc_start: 0.6180 (mp0) cc_final: 0.5963 (mp0) REVERT: B 35 TRP cc_start: 0.7233 (OUTLIER) cc_final: 0.6626 (m-10) REVERT: B 162 PHE cc_start: 0.6932 (t80) cc_final: 0.6526 (t80) REVERT: B 321 ASP cc_start: 0.7237 (p0) cc_final: 0.7023 (p0) REVERT: B 525 TRP cc_start: 0.7464 (p90) cc_final: 0.7233 (p90) REVERT: B 602 PHE cc_start: 0.8180 (t80) cc_final: 0.7919 (t80) REVERT: B 615 LEU cc_start: 0.6594 (mt) cc_final: 0.6081 (mt) REVERT: B 715 TYR cc_start: 0.7794 (t80) cc_final: 0.7576 (t80) REVERT: B 977 TRP cc_start: 0.5326 (t60) cc_final: 0.4920 (t-100) outliers start: 26 outliers final: 8 residues processed: 235 average time/residue: 1.3174 time to fit residues: 333.2774 Evaluate side-chains 219 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 140 LYS Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 998 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 108 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 53 ASN B 450 GLN B1125 HIS B1126 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.181098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.166601 restraints weight = 15312.510| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.74 r_work: 0.4104 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3972 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11459 Z= 0.257 Angle : 0.679 9.917 15546 Z= 0.347 Chirality : 0.047 0.180 1752 Planarity : 0.006 0.058 2032 Dihedral : 5.157 27.963 1580 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.51 % Allowed : 14.41 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.65 (0.22), residues: 1429 helix: 0.46 (0.18), residues: 763 sheet: -1.27 (0.43), residues: 147 loop : -1.44 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 35 HIS 0.010 0.001 HIS A 167 PHE 0.023 0.002 PHE B 106 TYR 0.040 0.003 TYR B 874 ARG 0.007 0.001 ARG B1151 Details of bonding type rmsd hydrogen bonds : bond 0.04757 ( 605) hydrogen bonds : angle 5.22885 ( 1776) covalent geometry : bond 0.00590 (11459) covalent geometry : angle 0.67855 (15546) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 214 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1213 (tpp) cc_final: 0.1011 (tpp) REVERT: A 179 GLN cc_start: 0.7308 (mt0) cc_final: 0.7015 (mm-40) REVERT: B 35 TRP cc_start: 0.7401 (OUTLIER) cc_final: 0.6769 (m-10) REVERT: B 525 TRP cc_start: 0.7580 (p90) cc_final: 0.7307 (p90) REVERT: B 602 PHE cc_start: 0.8287 (t80) cc_final: 0.8031 (t80) REVERT: B 615 LEU cc_start: 0.6842 (mt) cc_final: 0.6634 (mt) REVERT: B 641 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5573 (mm) REVERT: B 647 LYS cc_start: 0.6740 (mtmm) cc_final: 0.6495 (mttp) REVERT: B 715 TYR cc_start: 0.7889 (t80) cc_final: 0.7609 (t80) REVERT: B 852 LYS cc_start: 0.7243 (tttt) cc_final: 0.6956 (tttt) REVERT: B 965 GLN cc_start: 0.6224 (OUTLIER) cc_final: 0.5598 (tt0) REVERT: B 983 ARG cc_start: 0.6743 (ttp80) cc_final: 0.6446 (ttp-110) outliers start: 30 outliers final: 9 residues processed: 225 average time/residue: 1.3588 time to fit residues: 330.3514 Evaluate side-chains 224 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1139 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 33 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 130 optimal weight: 0.2980 chunk 106 optimal weight: 0.2980 chunk 86 optimal weight: 0.0060 chunk 133 optimal weight: 1.9990 chunk 117 optimal weight: 0.1980 chunk 39 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.2796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN B1125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.184937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.170724 restraints weight = 15312.273| |-----------------------------------------------------------------------------| r_work (start): 0.4237 rms_B_bonded: 1.73 r_work: 0.4154 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11459 Z= 0.132 Angle : 0.562 7.275 15546 Z= 0.293 Chirality : 0.042 0.166 1752 Planarity : 0.005 0.050 2032 Dihedral : 4.762 22.418 1578 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.51 % Allowed : 16.08 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1429 helix: 0.78 (0.19), residues: 769 sheet: -1.34 (0.42), residues: 148 loop : -1.29 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 35 HIS 0.005 0.001 HIS B 260 PHE 0.022 0.002 PHE B 106 TYR 0.047 0.002 TYR B 874 ARG 0.007 0.000 ARG B1151 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 605) hydrogen bonds : angle 4.92089 ( 1776) covalent geometry : bond 0.00296 (11459) covalent geometry : angle 0.56187 (15546) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.0959 (tpp) cc_final: 0.0743 (tpp) REVERT: A 179 GLN cc_start: 0.7309 (mt0) cc_final: 0.6976 (mm-40) REVERT: B 35 TRP cc_start: 0.7293 (OUTLIER) cc_final: 0.6674 (m-10) REVERT: B 307 LEU cc_start: 0.8366 (mt) cc_final: 0.8124 (mt) REVERT: B 359 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7945 (pp) REVERT: B 525 TRP cc_start: 0.7541 (p90) cc_final: 0.7264 (p90) REVERT: B 602 PHE cc_start: 0.8249 (t80) cc_final: 0.8013 (t80) REVERT: B 715 TYR cc_start: 0.7731 (t80) cc_final: 0.7500 (t80) REVERT: B 979 MET cc_start: 0.6161 (mtt) cc_final: 0.4907 (mpt) outliers start: 30 outliers final: 9 residues processed: 220 average time/residue: 1.2574 time to fit residues: 298.4965 Evaluate side-chains 208 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 197 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 684 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 114 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 103 optimal weight: 9.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.182681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.168483 restraints weight = 15177.902| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 1.72 r_work: 0.4124 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11459 Z= 0.209 Angle : 0.630 7.740 15546 Z= 0.326 Chirality : 0.045 0.165 1752 Planarity : 0.006 0.058 2032 Dihedral : 4.903 22.614 1578 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.76 % Allowed : 17.09 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.40 (0.22), residues: 1429 helix: 0.66 (0.18), residues: 766 sheet: -1.21 (0.43), residues: 147 loop : -1.29 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 35 HIS 0.008 0.001 HIS A 167 PHE 0.024 0.002 PHE B 106 TYR 0.051 0.003 TYR B 874 ARG 0.009 0.001 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 605) hydrogen bonds : angle 5.04701 ( 1776) covalent geometry : bond 0.00484 (11459) covalent geometry : angle 0.62972 (15546) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.0958 (tpp) cc_final: 0.0749 (tpp) REVERT: A 179 GLN cc_start: 0.7419 (mt0) cc_final: 0.7110 (mm110) REVERT: B 35 TRP cc_start: 0.7346 (OUTLIER) cc_final: 0.6738 (m-10) REVERT: B 359 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7954 (pp) REVERT: B 525 TRP cc_start: 0.7566 (p90) cc_final: 0.7320 (p90) REVERT: B 602 PHE cc_start: 0.8274 (t80) cc_final: 0.8018 (t80) REVERT: B 715 TYR cc_start: 0.7844 (t80) cc_final: 0.7549 (t80) REVERT: B 852 LYS cc_start: 0.7195 (tttt) cc_final: 0.6909 (tttt) outliers start: 33 outliers final: 12 residues processed: 227 average time/residue: 1.3216 time to fit residues: 323.4267 Evaluate side-chains 220 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 206 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 TYR Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 84 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 124 optimal weight: 0.3980 chunk 97 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS B1158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.183071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.168957 restraints weight = 15319.063| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 1.72 r_work: 0.4128 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3999 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11459 Z= 0.189 Angle : 0.623 8.613 15546 Z= 0.321 Chirality : 0.045 0.269 1752 Planarity : 0.005 0.056 2032 Dihedral : 4.876 23.105 1578 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.02 % Allowed : 18.59 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.36 (0.22), residues: 1429 helix: 0.65 (0.18), residues: 769 sheet: -1.06 (0.43), residues: 152 loop : -1.26 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 232 HIS 0.006 0.001 HIS A 167 PHE 0.025 0.002 PHE B 106 TYR 0.043 0.002 TYR B 874 ARG 0.008 0.001 ARG B1151 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 605) hydrogen bonds : angle 5.02754 ( 1776) covalent geometry : bond 0.00435 (11459) covalent geometry : angle 0.62255 (15546) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.7455 (mt0) cc_final: 0.7162 (mm110) REVERT: A 203 ARG cc_start: 0.7711 (ttm110) cc_final: 0.7436 (ttm-80) REVERT: B 35 TRP cc_start: 0.7351 (OUTLIER) cc_final: 0.6752 (m-10) REVERT: B 359 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7909 (pp) REVERT: B 521 TYR cc_start: 0.7632 (m-80) cc_final: 0.7425 (m-80) REVERT: B 525 TRP cc_start: 0.7567 (p90) cc_final: 0.7330 (p90) REVERT: B 591 ASP cc_start: 0.6852 (t0) cc_final: 0.6611 (t0) REVERT: B 602 PHE cc_start: 0.8269 (t80) cc_final: 0.8055 (t80) REVERT: B 615 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6724 (mt) REVERT: B 715 TYR cc_start: 0.7811 (t80) cc_final: 0.7509 (t80) REVERT: B 852 LYS cc_start: 0.7156 (tttt) cc_final: 0.6895 (tttt) outliers start: 36 outliers final: 15 residues processed: 223 average time/residue: 1.3538 time to fit residues: 326.7840 Evaluate side-chains 218 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain B residue 1139 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 131 optimal weight: 5.9990 chunk 62 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 50 optimal weight: 0.3980 chunk 34 optimal weight: 0.0000 chunk 52 optimal weight: 0.0570 chunk 132 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 overall best weight: 0.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS B1158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.185032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.170847 restraints weight = 15554.032| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 1.74 r_work: 0.4155 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4027 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11459 Z= 0.139 Angle : 0.592 7.124 15546 Z= 0.304 Chirality : 0.043 0.171 1752 Planarity : 0.005 0.049 2032 Dihedral : 4.689 22.903 1578 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.26 % Allowed : 19.77 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.13 (0.22), residues: 1429 helix: 0.90 (0.19), residues: 768 sheet: -1.03 (0.44), residues: 153 loop : -1.23 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 35 HIS 0.005 0.001 HIS B 260 PHE 0.023 0.002 PHE B 106 TYR 0.045 0.002 TYR B 874 ARG 0.009 0.001 ARG B1147 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 605) hydrogen bonds : angle 4.91601 ( 1776) covalent geometry : bond 0.00319 (11459) covalent geometry : angle 0.59195 (15546) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.7181 (t80) cc_final: 0.6164 (t80) REVERT: A 92 ASN cc_start: 0.4845 (m110) cc_final: 0.4549 (m-40) REVERT: A 179 GLN cc_start: 0.7399 (mt0) cc_final: 0.7039 (mm110) REVERT: A 203 ARG cc_start: 0.7584 (ttm110) cc_final: 0.7302 (ttm-80) REVERT: B 35 TRP cc_start: 0.7313 (OUTLIER) cc_final: 0.6701 (m-10) REVERT: B 359 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7910 (pp) REVERT: B 521 TYR cc_start: 0.7485 (m-80) cc_final: 0.7260 (m-80) REVERT: B 525 TRP cc_start: 0.7536 (p90) cc_final: 0.7271 (p90) REVERT: B 602 PHE cc_start: 0.8237 (t80) cc_final: 0.8027 (t80) REVERT: B 715 TYR cc_start: 0.7714 (t80) cc_final: 0.7453 (t80) REVERT: B 852 LYS cc_start: 0.7150 (tttt) cc_final: 0.6887 (tttt) REVERT: B 1166 LEU cc_start: 0.7519 (mp) cc_final: 0.7293 (mt) outliers start: 27 outliers final: 12 residues processed: 217 average time/residue: 1.2708 time to fit residues: 298.2130 Evaluate side-chains 217 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 203 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 7 optimal weight: 0.0170 chunk 135 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 53 optimal weight: 0.0030 chunk 132 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 overall best weight: 0.3628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.184953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.170780 restraints weight = 15447.112| |-----------------------------------------------------------------------------| r_work (start): 0.4235 rms_B_bonded: 1.74 r_work: 0.4152 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.4023 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11459 Z= 0.146 Angle : 0.603 9.022 15546 Z= 0.309 Chirality : 0.044 0.182 1752 Planarity : 0.005 0.048 2032 Dihedral : 4.678 23.282 1578 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.84 % Allowed : 21.11 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1429 helix: 0.96 (0.19), residues: 763 sheet: -1.05 (0.43), residues: 153 loop : -1.27 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 232 HIS 0.005 0.001 HIS B 260 PHE 0.022 0.002 PHE B 106 TYR 0.045 0.002 TYR B 874 ARG 0.006 0.000 ARG B1151 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 605) hydrogen bonds : angle 4.90733 ( 1776) covalent geometry : bond 0.00337 (11459) covalent geometry : angle 0.60343 (15546) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.7222 (t80) cc_final: 0.6219 (t80) REVERT: A 92 ASN cc_start: 0.4879 (m110) cc_final: 0.4605 (m-40) REVERT: A 179 GLN cc_start: 0.7404 (mt0) cc_final: 0.7049 (mm110) REVERT: A 206 ILE cc_start: 0.7541 (mt) cc_final: 0.7302 (tt) REVERT: B 35 TRP cc_start: 0.7321 (OUTLIER) cc_final: 0.6663 (m-10) REVERT: B 359 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7913 (pp) REVERT: B 521 TYR cc_start: 0.7566 (m-80) cc_final: 0.7311 (m-80) REVERT: B 525 TRP cc_start: 0.7545 (p90) cc_final: 0.7285 (p90) REVERT: B 602 PHE cc_start: 0.8192 (t80) cc_final: 0.7943 (t80) REVERT: B 715 TYR cc_start: 0.7725 (t80) cc_final: 0.7428 (t80) REVERT: B 852 LYS cc_start: 0.7119 (tttt) cc_final: 0.6850 (tttt) REVERT: B 1166 LEU cc_start: 0.7534 (mp) cc_final: 0.7296 (mt) outliers start: 22 outliers final: 12 residues processed: 216 average time/residue: 1.4599 time to fit residues: 339.9646 Evaluate side-chains 215 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 chunk 63 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS B1158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.182367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.168053 restraints weight = 15420.302| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 1.75 r_work: 0.4123 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3992 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 11459 Z= 0.211 Angle : 0.672 9.460 15546 Z= 0.341 Chirality : 0.046 0.225 1752 Planarity : 0.006 0.053 2032 Dihedral : 4.885 24.461 1578 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.01 % Allowed : 21.27 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.35 (0.22), residues: 1429 helix: 0.73 (0.19), residues: 760 sheet: -1.01 (0.44), residues: 152 loop : -1.35 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 232 HIS 0.008 0.001 HIS A 167 PHE 0.026 0.002 PHE B 106 TYR 0.055 0.003 TYR B 874 ARG 0.010 0.001 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 605) hydrogen bonds : angle 5.08300 ( 1776) covalent geometry : bond 0.00490 (11459) covalent geometry : angle 0.67153 (15546) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 205 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.7323 (t80) cc_final: 0.6240 (t80) REVERT: A 179 GLN cc_start: 0.7476 (mt0) cc_final: 0.7108 (mm110) REVERT: A 206 ILE cc_start: 0.7693 (mt) cc_final: 0.7451 (tt) REVERT: B 35 TRP cc_start: 0.7402 (OUTLIER) cc_final: 0.6755 (m-10) REVERT: B 525 TRP cc_start: 0.7607 (p90) cc_final: 0.7350 (p90) REVERT: B 602 PHE cc_start: 0.8305 (t80) cc_final: 0.8091 (t80) REVERT: B 715 TYR cc_start: 0.7853 (t80) cc_final: 0.7526 (t80) REVERT: B 794 GLN cc_start: 0.7862 (tp40) cc_final: 0.7593 (tp-100) REVERT: B 852 LYS cc_start: 0.7129 (tttt) cc_final: 0.6865 (tttt) REVERT: B 979 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5802 (mtt) outliers start: 24 outliers final: 14 residues processed: 216 average time/residue: 1.3517 time to fit residues: 318.2032 Evaluate side-chains 216 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 548 LYS Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 874 TYR Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 979 MET Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain B residue 1139 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 52 optimal weight: 0.0010 chunk 7 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 29 optimal weight: 0.0870 chunk 19 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 overall best weight: 0.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS B1158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.184645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.170622 restraints weight = 15280.784| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 1.73 r_work: 0.4150 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4022 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.4022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11459 Z= 0.151 Angle : 0.636 10.796 15546 Z= 0.322 Chirality : 0.044 0.200 1752 Planarity : 0.005 0.050 2032 Dihedral : 4.756 24.155 1578 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.42 % Allowed : 21.94 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.22 (0.22), residues: 1429 helix: 0.86 (0.19), residues: 764 sheet: -1.04 (0.44), residues: 154 loop : -1.33 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 232 HIS 0.005 0.001 HIS B 260 PHE 0.025 0.002 PHE B 106 TYR 0.051 0.002 TYR B 874 ARG 0.012 0.001 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 605) hydrogen bonds : angle 4.97233 ( 1776) covalent geometry : bond 0.00351 (11459) covalent geometry : angle 0.63601 (15546) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2858 Ramachandran restraints generated. 1429 Oldfield, 0 Emsley, 1429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 1.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.7306 (t80) cc_final: 0.6290 (t80) REVERT: A 179 GLN cc_start: 0.7427 (mt0) cc_final: 0.7076 (mm110) REVERT: B 35 TRP cc_start: 0.7356 (OUTLIER) cc_final: 0.6705 (m-10) REVERT: B 525 TRP cc_start: 0.7544 (p90) cc_final: 0.7288 (p90) REVERT: B 602 PHE cc_start: 0.8250 (t80) cc_final: 0.8001 (t80) REVERT: B 715 TYR cc_start: 0.7717 (t80) cc_final: 0.7433 (t80) REVERT: B 794 GLN cc_start: 0.7861 (tp40) cc_final: 0.7581 (tp-100) REVERT: B 852 LYS cc_start: 0.7090 (tttt) cc_final: 0.6836 (tttt) REVERT: B 1166 LEU cc_start: 0.7473 (mp) cc_final: 0.7240 (mt) outliers start: 17 outliers final: 13 residues processed: 202 average time/residue: 1.3804 time to fit residues: 303.2130 Evaluate side-chains 206 residues out of total 1194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 548 LYS Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 874 TYR Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 1064 HIS Chi-restraints excluded: chain B residue 1133 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 100 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 48 optimal weight: 0.4980 chunk 19 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.183711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.169550 restraints weight = 15210.813| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 1.73 r_work: 0.4137 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.4007 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 11459 Z= 0.185 Angle : 0.678 13.416 15546 Z= 0.338 Chirality : 0.045 0.210 1752 Planarity : 0.005 0.053 2032 Dihedral : 4.837 24.840 1578 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.51 % Allowed : 21.94 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: -0.33 (0.22), residues: 1429 helix: 0.76 (0.19), residues: 765 sheet: -1.12 (0.43), residues: 154 loop : -1.35 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 232 HIS 0.007 0.001 HIS A 167 PHE 0.026 0.002 PHE B 106 TYR 0.053 0.003 TYR B 874 ARG 0.014 0.001 ARG B 360 Details of bonding type rmsd hydrogen bonds : bond 0.04014 ( 605) hydrogen bonds : angle 5.04441 ( 1776) covalent geometry : bond 0.00430 (11459) covalent geometry : angle 0.67824 (15546) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10755.17 seconds wall clock time: 187 minutes 46.43 seconds (11266.43 seconds total)