Starting phenix.real_space_refine on Sun Apr 7 18:49:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/04_2024/8vx9_43613.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/04_2024/8vx9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/04_2024/8vx9_43613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/04_2024/8vx9_43613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/04_2024/8vx9_43613.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/04_2024/8vx9_43613.pdb" } 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 Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 6.29, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 4.58 Conformation dependent library (CDL) restraints added in 2.2 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: 1.52 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: 4.43 Time building geometry restraints manager: 4.96 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: 99.67 - 106.56: 314 106.56 - 113.44: 6338 113.44 - 120.33: 4151 120.33 - 127.21: 4611 127.21 - 134.10: 132 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 2.520 nonbonded pdb=" O GLY B 389 " pdb=" NZ LYS B 410 " model vdw 2.226 2.520 nonbonded pdb=" O THR A 100 " pdb=" NZ LYS A 103 " model vdw 2.240 2.520 nonbonded pdb=" OD1 ASP B 591 " pdb=" NH1 ARG B 595 " model vdw 2.254 2.520 nonbonded pdb=" NZ LYS A 108 " pdb=" OD2 ASP B 200 " model vdw 2.285 2.520 ... (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 ========== 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: 1.430 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: 6.620 Check model and map are aligned: 0.170 Set scattering table: 0.120 Process input model: 33.860 Find NCS groups from input model: 0.310 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: 0.000 Load rotamer database and sin/cos tables:13.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.640 ------------------------------------------------------------------------------- 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= 0.253 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 *********************** 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 fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 1.208 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: 1.3197 time to fit residues: 369.1480 Evaluate side-chains 228 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 1.276 ------------------------------------------------------------------------------- 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: 0.9990 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.1980 chunk 72 optimal weight: 0.0980 chunk 57 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 chunk 43 optimal weight: 0.1980 chunk 67 optimal weight: 0.2980 chunk 82 optimal weight: 0.9980 chunk 128 optimal weight: 0.6980 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 ASN B 178 GLN B 423 ASN B 494 ASN B 725 GLN ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11459 Z= 0.204 Angle : 0.590 11.220 15546 Z= 0.300 Chirality : 0.043 0.155 1752 Planarity : 0.005 0.045 2032 Dihedral : 5.321 90.541 1582 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.09 % Allowed : 9.97 % Favored : 87.94 % 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: -0.25 (0.22), residues: 1429 helix: 0.84 (0.19), residues: 767 sheet: -1.21 (0.43), residues: 144 loop : -1.31 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 977 HIS 0.006 0.001 HIS B 260 PHE 0.022 0.002 PHE B1046 TYR 0.021 0.002 TYR B 874 ARG 0.004 0.000 ARG B1151 *********************** 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 254 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 229 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1191 (tpp) cc_final: 0.0941 (tpp) REVERT: A 19 TYR cc_start: 0.7456 (t80) cc_final: 0.6482 (t80) REVERT: A 140 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7623 (mmmt) REVERT: A 186 LYS cc_start: 0.6815 (mttp) cc_final: 0.6601 (mttp) REVERT: B 162 PHE cc_start: 0.6912 (t80) cc_final: 0.6515 (t80) REVERT: B 359 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8067 (pp) REVERT: B 602 PHE cc_start: 0.8077 (t80) cc_final: 0.7818 (t80) REVERT: B 715 TYR cc_start: 0.7910 (t80) cc_final: 0.7708 (t80) REVERT: B 927 PHE cc_start: 0.5432 (m-10) cc_final: 0.5136 (m-10) REVERT: B 977 TRP cc_start: 0.5317 (t60) cc_final: 0.4910 (t-100) REVERT: B 1078 MET cc_start: 0.6075 (mmt) cc_final: 0.5819 (mmt) outliers start: 25 outliers final: 9 residues processed: 237 average time/residue: 1.3478 time to fit residues: 344.1135 Evaluate side-chains 228 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 217 time to evaluate : 1.229 ------------------------------------------------------------------------------- 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 A residue 177 ASN Chi-restraints excluded: chain B residue 359 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 998 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 35 optimal weight: 0.4980 chunk 129 optimal weight: 3.9990 chunk 139 optimal weight: 0.0770 chunk 115 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 177 ASN B 423 ASN B 450 GLN B 840 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS B1126 HIS B1158 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11459 Z= 0.363 Angle : 0.651 8.345 15546 Z= 0.334 Chirality : 0.046 0.162 1752 Planarity : 0.006 0.053 2032 Dihedral : 5.033 27.669 1580 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.68 % Allowed : 14.32 % Favored : 83.00 % 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: -0.54 (0.22), residues: 1429 helix: 0.54 (0.19), residues: 763 sheet: -1.20 (0.43), residues: 147 loop : -1.36 (0.26), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1105 HIS 0.009 0.001 HIS A 167 PHE 0.019 0.002 PHE B 106 TYR 0.040 0.003 TYR B 874 ARG 0.009 0.001 ARG B 696 *********************** 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 250 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1177 (tpp) cc_final: 0.0946 (tpp) REVERT: B 35 TRP cc_start: 0.7519 (OUTLIER) cc_final: 0.6945 (m-10) REVERT: B 353 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.8007 (t) REVERT: B 359 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8092 (pp) REVERT: B 602 PHE cc_start: 0.8173 (t80) cc_final: 0.7916 (t80) REVERT: B 715 TYR cc_start: 0.8037 (t80) cc_final: 0.7752 (t80) REVERT: B 852 LYS cc_start: 0.7158 (tttt) cc_final: 0.6915 (tttt) REVERT: B 890 ILE cc_start: 0.7990 (pt) cc_final: 0.7739 (pp) REVERT: B 927 PHE cc_start: 0.5700 (m-10) cc_final: 0.5399 (m-10) outliers start: 32 outliers final: 11 residues processed: 228 average time/residue: 1.3043 time to fit residues: 320.9627 Evaluate side-chains 226 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 313 GLU Chi-restraints excluded: chain B residue 353 VAL 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 958 THR Chi-restraints excluded: chain B residue 1023 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 122 optimal weight: 0.2980 chunk 36 optimal weight: 0.0980 chunk 114 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 ASN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11459 Z= 0.217 Angle : 0.571 11.272 15546 Z= 0.295 Chirality : 0.043 0.156 1752 Planarity : 0.005 0.047 2032 Dihedral : 4.767 21.891 1578 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.18 % Allowed : 16.58 % Favored : 81.24 % 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: 0.73 (0.19), residues: 770 sheet: -1.25 (0.42), residues: 149 loop : -1.26 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1105 HIS 0.006 0.001 HIS B 260 PHE 0.022 0.002 PHE B 106 TYR 0.048 0.002 TYR B 874 ARG 0.006 0.000 ARG B 696 *********************** 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 235 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 209 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1071 (tpp) cc_final: 0.0854 (tpp) REVERT: B 35 TRP cc_start: 0.7432 (OUTLIER) cc_final: 0.6873 (m-10) REVERT: B 359 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8050 (pp) REVERT: B 602 PHE cc_start: 0.8145 (t80) cc_final: 0.7893 (t80) REVERT: B 715 TYR cc_start: 0.7927 (t80) cc_final: 0.7682 (t80) REVERT: B 890 ILE cc_start: 0.7969 (pt) cc_final: 0.7715 (pp) REVERT: B 927 PHE cc_start: 0.5604 (m-10) cc_final: 0.5221 (m-10) REVERT: B 979 MET cc_start: 0.6236 (mtt) cc_final: 0.4970 (mpt) outliers start: 26 outliers final: 11 residues processed: 220 average time/residue: 1.3184 time to fit residues: 313.4593 Evaluate side-chains 217 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 204 time to evaluate : 1.223 ------------------------------------------------------------------------------- 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 145 MET Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 152 LEU 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 958 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 117 optimal weight: 0.4980 chunk 94 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN B 423 ASN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11459 Z= 0.336 Angle : 0.640 8.064 15546 Z= 0.330 Chirality : 0.045 0.162 1752 Planarity : 0.005 0.062 2032 Dihedral : 4.946 23.582 1578 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.93 % Allowed : 17.09 % Favored : 79.98 % 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: -0.51 (0.22), residues: 1429 helix: 0.58 (0.19), residues: 763 sheet: -1.27 (0.43), residues: 149 loop : -1.34 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 525 HIS 0.009 0.002 HIS A 167 PHE 0.025 0.002 PHE B 106 TYR 0.057 0.003 TYR B 874 ARG 0.008 0.001 ARG B 696 *********************** 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 251 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 216 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.0937 (tpp) cc_final: 0.0715 (tpp) REVERT: B 35 TRP cc_start: 0.7499 (OUTLIER) cc_final: 0.6944 (m-10) REVERT: B 359 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8056 (pp) REVERT: B 602 PHE cc_start: 0.8174 (t80) cc_final: 0.7903 (t80) REVERT: B 852 LYS cc_start: 0.7140 (tttt) cc_final: 0.6912 (tttt) REVERT: B 890 ILE cc_start: 0.7991 (pt) cc_final: 0.7765 (pp) REVERT: B 927 PHE cc_start: 0.5758 (m-10) cc_final: 0.5443 (m-10) REVERT: B 979 MET cc_start: 0.6293 (mtt) cc_final: 0.4896 (mpt) REVERT: B 983 ARG cc_start: 0.6668 (ttp80) cc_final: 0.6338 (ttp-110) outliers start: 35 outliers final: 20 residues processed: 232 average time/residue: 1.2987 time to fit residues: 325.7204 Evaluate side-chains 234 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 212 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 145 MET Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 152 LEU 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 620 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 973 TYR Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1139 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 137 optimal weight: 0.0980 chunk 114 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 423 ASN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11459 Z= 0.243 Angle : 0.588 6.877 15546 Z= 0.306 Chirality : 0.043 0.227 1752 Planarity : 0.005 0.051 2032 Dihedral : 4.785 24.090 1578 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.09 % Allowed : 18.59 % Favored : 79.31 % 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: 0.74 (0.19), residues: 766 sheet: -1.18 (0.42), residues: 154 loop : -1.28 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 525 HIS 0.006 0.001 HIS B 260 PHE 0.024 0.002 PHE B 106 TYR 0.046 0.002 TYR B 874 ARG 0.011 0.000 ARG B 312 *********************** 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 236 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 211 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.0931 (tpp) cc_final: 0.0719 (tpp) REVERT: A 92 ASN cc_start: 0.4829 (m110) cc_final: 0.4618 (m-40) REVERT: B 35 TRP cc_start: 0.7462 (OUTLIER) cc_final: 0.6871 (m-10) REVERT: B 300 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7659 (mtt180) REVERT: B 359 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8079 (pp) REVERT: B 602 PHE cc_start: 0.8160 (t80) cc_final: 0.7896 (t80) REVERT: B 715 TYR cc_start: 0.7974 (t80) cc_final: 0.7713 (t80) REVERT: B 852 LYS cc_start: 0.7116 (tttt) cc_final: 0.6876 (tttt) REVERT: B 890 ILE cc_start: 0.7988 (pt) cc_final: 0.7746 (pp) REVERT: B 927 PHE cc_start: 0.5685 (m-10) cc_final: 0.5363 (m-10) outliers start: 25 outliers final: 14 residues processed: 221 average time/residue: 1.3123 time to fit residues: 313.3883 Evaluate side-chains 221 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 204 time to evaluate : 1.299 ------------------------------------------------------------------------------- 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 145 MET Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 300 ARG 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 0.0000 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 136 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11459 Z= 0.256 Angle : 0.613 13.687 15546 Z= 0.313 Chirality : 0.044 0.177 1752 Planarity : 0.005 0.050 2032 Dihedral : 4.768 24.533 1578 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.26 % Allowed : 20.02 % Favored : 77.72 % 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: -0.31 (0.22), residues: 1429 helix: 0.77 (0.19), residues: 766 sheet: -1.20 (0.41), residues: 154 loop : -1.30 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 525 HIS 0.006 0.001 HIS A 167 PHE 0.025 0.002 PHE B 106 TYR 0.048 0.002 TYR B 874 ARG 0.009 0.000 ARG B1147 *********************** 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 228 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 TRP cc_start: 0.7473 (OUTLIER) cc_final: 0.6888 (m-10) REVERT: B 300 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7809 (mtt180) REVERT: B 359 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8064 (pp) REVERT: B 602 PHE cc_start: 0.8159 (t80) cc_final: 0.7896 (t80) REVERT: B 618 GLU cc_start: 0.7569 (mp0) cc_final: 0.7249 (pm20) REVERT: B 647 LYS cc_start: 0.6478 (mttp) cc_final: 0.6184 (mmtm) REVERT: B 715 TYR cc_start: 0.7980 (t80) cc_final: 0.7675 (t80) REVERT: B 852 LYS cc_start: 0.7101 (tttt) cc_final: 0.6866 (tttt) REVERT: B 890 ILE cc_start: 0.7986 (pt) cc_final: 0.7758 (pp) REVERT: B 927 PHE cc_start: 0.5735 (m-10) cc_final: 0.5434 (m-10) REVERT: B 1166 LEU cc_start: 0.7782 (mp) cc_final: 0.7554 (mt) outliers start: 27 outliers final: 13 residues processed: 214 average time/residue: 1.3884 time to fit residues: 321.3775 Evaluate side-chains 215 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 199 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 A residue 145 MET Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 300 ARG 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 874 TYR Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 TYR Chi-restraints excluded: chain B residue 1023 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 chunk 67 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11459 Z= 0.244 Angle : 0.624 16.430 15546 Z= 0.315 Chirality : 0.044 0.189 1752 Planarity : 0.005 0.051 2032 Dihedral : 4.734 24.768 1578 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.93 % Allowed : 21.27 % Favored : 76.80 % 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: -0.24 (0.22), residues: 1429 helix: 0.81 (0.19), residues: 768 sheet: -1.16 (0.41), residues: 154 loop : -1.27 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 525 HIS 0.006 0.001 HIS A 167 PHE 0.025 0.002 PHE B 106 TYR 0.048 0.002 TYR B 874 ARG 0.010 0.000 ARG B1147 *********************** 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 224 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 201 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 TRP cc_start: 0.7467 (OUTLIER) cc_final: 0.6886 (m-10) REVERT: B 300 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.7798 (mtt180) REVERT: B 359 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7953 (pp) REVERT: B 602 PHE cc_start: 0.8155 (t80) cc_final: 0.7939 (t80) REVERT: B 618 GLU cc_start: 0.7584 (mp0) cc_final: 0.7236 (pm20) REVERT: B 715 TYR cc_start: 0.7924 (t80) cc_final: 0.7630 (t80) REVERT: B 852 LYS cc_start: 0.7103 (tttt) cc_final: 0.6859 (tttt) REVERT: B 890 ILE cc_start: 0.8211 (pt) cc_final: 0.7934 (pp) REVERT: B 927 PHE cc_start: 0.5720 (m-10) cc_final: 0.5460 (m-10) REVERT: B 1166 LEU cc_start: 0.7767 (mp) cc_final: 0.7549 (mt) outliers start: 23 outliers final: 15 residues processed: 211 average time/residue: 1.3119 time to fit residues: 299.0937 Evaluate side-chains 219 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 201 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 145 MET Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 300 ARG 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 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 1023 LEU Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 55 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN B 423 ASN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11459 Z= 0.357 Angle : 0.692 17.044 15546 Z= 0.348 Chirality : 0.046 0.237 1752 Planarity : 0.005 0.060 2032 Dihedral : 4.963 25.784 1578 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.09 % Allowed : 22.03 % Favored : 75.88 % 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: -0.49 (0.22), residues: 1429 helix: 0.57 (0.19), residues: 766 sheet: -1.21 (0.42), residues: 154 loop : -1.32 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 525 HIS 0.009 0.001 HIS A 167 PHE 0.027 0.002 PHE B 106 TYR 0.051 0.003 TYR B 874 ARG 0.011 0.001 ARG B1147 *********************** 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 232 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 35 TRP cc_start: 0.7556 (OUTLIER) cc_final: 0.6964 (m-10) REVERT: B 300 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7801 (mtt180) REVERT: B 359 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8037 (pp) REVERT: B 602 PHE cc_start: 0.8194 (t80) cc_final: 0.7964 (t80) REVERT: B 852 LYS cc_start: 0.7119 (tttt) cc_final: 0.6888 (tttt) REVERT: B 890 ILE cc_start: 0.8218 (pt) cc_final: 0.7960 (pp) REVERT: B 1063 SER cc_start: 0.5670 (OUTLIER) cc_final: 0.4728 (t) REVERT: B 1128 LEU cc_start: 0.6410 (OUTLIER) cc_final: 0.6044 (mt) REVERT: B 1166 LEU cc_start: 0.7848 (mp) cc_final: 0.7625 (mt) outliers start: 25 outliers final: 15 residues processed: 217 average time/residue: 1.3155 time to fit residues: 308.1666 Evaluate side-chains 225 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 205 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 300 ARG 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 620 LEU 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 973 TYR Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1063 SER Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 112 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 87 optimal weight: 0.3980 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN B 423 ASN ** B 794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11459 Z= 0.250 Angle : 0.647 15.919 15546 Z= 0.326 Chirality : 0.044 0.213 1752 Planarity : 0.005 0.059 2032 Dihedral : 4.799 24.904 1578 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.76 % Allowed : 22.70 % Favored : 75.54 % 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: 0.74 (0.19), residues: 770 sheet: -1.18 (0.42), residues: 154 loop : -1.29 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B 525 HIS 0.006 0.001 HIS B 260 PHE 0.026 0.002 PHE B 106 TYR 0.048 0.002 TYR B 874 ARG 0.017 0.001 ARG B 360 ********************** 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 220 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 237 ARG cc_start: 0.7425 (ttt-90) cc_final: 0.7099 (ttt90) REVERT: B 35 TRP cc_start: 0.7500 (OUTLIER) cc_final: 0.6891 (m-10) REVERT: B 300 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.7820 (mtt180) REVERT: B 359 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.7898 (pp) REVERT: B 595 ARG cc_start: 0.6765 (mtp85) cc_final: 0.6563 (mtt-85) REVERT: B 602 PHE cc_start: 0.8162 (t80) cc_final: 0.7947 (t80) REVERT: B 852 LYS cc_start: 0.7104 (tttt) cc_final: 0.6866 (tttt) REVERT: B 890 ILE cc_start: 0.8202 (pt) cc_final: 0.7916 (pp) REVERT: B 927 PHE cc_start: 0.5694 (m-10) cc_final: 0.5480 (m-10) REVERT: B 1166 LEU cc_start: 0.7778 (mp) cc_final: 0.7537 (mt) outliers start: 21 outliers final: 15 residues processed: 209 average time/residue: 1.3361 time to fit residues: 302.2869 Evaluate side-chains 212 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain B residue 35 TRP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 256 PHE Chi-restraints excluded: chain B residue 300 ARG 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 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 973 TYR Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1128 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 14 optimal weight: 0.0070 chunk 20 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 450 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 = 0.4373 r_free = 0.4373 target = 0.183466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.169450 restraints weight = 15180.979| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 1.68 r_work: 0.4135 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.4008 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.4008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.2590 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= 0.302 Angle : 0.676 14.682 15546 Z= 0.340 Chirality : 0.045 0.223 1752 Planarity : 0.005 0.053 2032 Dihedral : 4.865 24.875 1578 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.59 % Allowed : 22.78 % Favored : 75.63 % 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: -0.40 (0.22), residues: 1429 helix: 0.68 (0.19), residues: 768 sheet: -1.22 (0.42), residues: 154 loop : -1.32 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 525 HIS 0.008 0.001 HIS A 167 PHE 0.027 0.002 PHE B 106 TYR 0.050 0.003 TYR B 874 ARG 0.012 0.000 ARG B1147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5345.92 seconds wall clock time: 95 minutes 54.03 seconds (5754.03 seconds total)