Starting phenix.real_space_refine on Sun Aug 4 19:44:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/08_2024/8vx9_43613.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/08_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_43613/08_2024/8vx9_43613.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/08_2024/8vx9_43613.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/08_2024/8vx9_43613.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vx9_43613/08_2024/8vx9_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 Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 7.05, per 1000 atoms: 0.63 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: 4.51 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: 1.35 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: 4.19 Time building geometry restraints manager: 5.01 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 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: 5.200 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: 0.430 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 34.660 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.830 ------------------------------------------------------------------------------- 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 : 1.165 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: 1.2231 time to fit residues: 342.2393 Evaluate side-chains 228 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 226 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 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= 0.238 Angle : 0.619 10.438 15546 Z= 0.318 Chirality : 0.044 0.165 1752 Planarity : 0.005 0.062 2032 Dihedral : 5.340 82.097 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 *********************** 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 fitting. rotamer outliers: 26 poor density : 227 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.1183 (tpp) cc_final: 0.0941 (tpp) REVERT: A 140 LYS cc_start: 0.7909 (OUTLIER) cc_final: 0.7661 (mmmt) REVERT: A 179 GLN cc_start: 0.6958 (mt0) cc_final: 0.6756 (mm-40) REVERT: A 182 GLU cc_start: 0.6202 (mp0) cc_final: 0.5951 (mp0) REVERT: B 35 TRP cc_start: 0.7414 (OUTLIER) cc_final: 0.6830 (m-10) REVERT: B 162 PHE cc_start: 0.6899 (t80) cc_final: 0.6512 (t80) REVERT: B 321 ASP cc_start: 0.7274 (p0) cc_final: 0.7068 (p0) REVERT: B 359 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8091 (pp) REVERT: B 525 TRP cc_start: 0.7487 (p90) cc_final: 0.7279 (p90) REVERT: B 602 PHE cc_start: 0.8087 (t80) cc_final: 0.7815 (t80) REVERT: B 615 LEU cc_start: 0.6734 (mt) cc_final: 0.6251 (mt) REVERT: B 715 TYR cc_start: 0.7941 (t80) cc_final: 0.7707 (t80) REVERT: B 821 GLN cc_start: 0.7110 (mm-40) cc_final: 0.6901 (mm-40) REVERT: B 927 PHE cc_start: 0.5375 (m-10) cc_final: 0.5097 (m-10) REVERT: B 977 TRP cc_start: 0.5319 (t60) cc_final: 0.4923 (t-100) outliers start: 26 outliers final: 8 residues processed: 235 average time/residue: 1.2957 time to fit residues: 328.9795 Evaluate side-chains 220 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 209 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 A residue 140 LYS Chi-restraints excluded: chain B residue 35 TRP 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: 0.7980 chunk 87 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 139 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.1869 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= 0.332 Angle : 0.645 9.142 15546 Z= 0.331 Chirality : 0.046 0.174 1752 Planarity : 0.006 0.050 2032 Dihedral : 5.036 27.289 1580 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.43 % Allowed : 14.32 % Favored : 83.25 % 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: -0.53 (0.22), residues: 1429 helix: 0.56 (0.19), residues: 768 sheet: -1.25 (0.43), residues: 147 loop : -1.38 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 35 HIS 0.008 0.001 HIS A 167 PHE 0.022 0.002 PHE B 106 TYR 0.038 0.003 TYR B 874 ARG 0.007 0.001 ARG B1151 *********************** 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 fitting. rotamer outliers: 29 poor density : 215 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.7064 (mt0) cc_final: 0.6857 (mm-40) REVERT: B 35 TRP cc_start: 0.7493 (OUTLIER) cc_final: 0.6885 (m-10) REVERT: B 322 ASN cc_start: 0.7490 (m-40) cc_final: 0.7115 (m-40) REVERT: B 353 VAL cc_start: 0.8247 (OUTLIER) cc_final: 0.8031 (t) REVERT: B 359 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.8100 (pp) REVERT: B 525 TRP cc_start: 0.7564 (p90) cc_final: 0.7353 (p90) REVERT: B 602 PHE cc_start: 0.8169 (t80) cc_final: 0.7904 (t80) REVERT: B 615 LEU cc_start: 0.6977 (mt) cc_final: 0.6743 (mt) REVERT: B 647 LYS cc_start: 0.6557 (mtmm) cc_final: 0.6319 (mttp) REVERT: B 715 TYR cc_start: 0.8018 (t80) cc_final: 0.7715 (t80) REVERT: B 852 LYS cc_start: 0.7149 (tttt) cc_final: 0.6900 (tttt) REVERT: B 890 ILE cc_start: 0.8013 (pt) cc_final: 0.7765 (pp) REVERT: B 927 PHE cc_start: 0.5690 (m-10) cc_final: 0.5398 (m-10) REVERT: B 965 GLN cc_start: 0.5932 (OUTLIER) cc_final: 0.5593 (tt0) outliers start: 29 outliers final: 8 residues processed: 227 average time/residue: 1.2846 time to fit residues: 314.5225 Evaluate side-chains 223 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 211 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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 965 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 0.0970 chunk 97 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.0770 chunk 129 optimal weight: 0.5980 chunk 137 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 114 optimal weight: 0.5980 overall best weight: 0.2936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1125 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11459 Z= 0.200 Angle : 0.562 6.517 15546 Z= 0.293 Chirality : 0.042 0.154 1752 Planarity : 0.005 0.049 2032 Dihedral : 4.739 22.011 1578 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.18 % Allowed : 16.33 % Favored : 81.49 % 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: -0.29 (0.22), residues: 1429 helix: 0.80 (0.19), residues: 771 sheet: -1.34 (0.42), residues: 148 loop : -1.28 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 35 HIS 0.005 0.001 HIS B 260 PHE 0.022 0.002 PHE B 106 TYR 0.048 0.002 TYR B 874 ARG 0.007 0.000 ARG B 595 *********************** 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 : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.7032 (mt0) cc_final: 0.6825 (mm110) REVERT: B 35 TRP cc_start: 0.7423 (OUTLIER) cc_final: 0.6840 (m-10) REVERT: B 359 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7955 (pp) REVERT: B 525 TRP cc_start: 0.7544 (p90) cc_final: 0.7331 (p90) REVERT: B 602 PHE cc_start: 0.8099 (t80) cc_final: 0.7838 (t80) REVERT: B 715 TYR cc_start: 0.7906 (t80) cc_final: 0.7648 (t80) REVERT: B 927 PHE cc_start: 0.5555 (m-10) cc_final: 0.5203 (m-10) REVERT: B 979 MET cc_start: 0.6173 (mtt) cc_final: 0.5142 (mpt) outliers start: 26 outliers final: 7 residues processed: 221 average time/residue: 1.2539 time to fit residues: 298.9183 Evaluate side-chains 209 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 200 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 608 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 117 optimal weight: 0.5980 chunk 94 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 123 optimal weight: 0.0570 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 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: 0.6752 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11459 Z= 0.228 Angle : 0.579 6.523 15546 Z= 0.300 Chirality : 0.043 0.158 1752 Planarity : 0.005 0.057 2032 Dihedral : 4.695 21.528 1578 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.60 % Allowed : 17.92 % Favored : 79.48 % 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: -0.18 (0.22), residues: 1429 helix: 0.87 (0.19), residues: 769 sheet: -1.23 (0.43), residues: 148 loop : -1.21 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 35 HIS 0.005 0.001 HIS A 167 PHE 0.022 0.002 PHE B 106 TYR 0.047 0.002 TYR B 874 ARG 0.009 0.000 ARG B 360 *********************** 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 241 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 210 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.7086 (mt0) cc_final: 0.6840 (mm110) REVERT: B 35 TRP cc_start: 0.7405 (OUTLIER) cc_final: 0.6823 (m-10) REVERT: B 359 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.8029 (pp) REVERT: B 525 TRP cc_start: 0.7565 (p90) cc_final: 0.7338 (p90) REVERT: B 602 PHE cc_start: 0.8107 (t80) cc_final: 0.7840 (t80) REVERT: B 715 TYR cc_start: 0.7919 (t80) cc_final: 0.7624 (t80) REVERT: B 867 THR cc_start: 0.8146 (OUTLIER) cc_final: 0.7941 (t) REVERT: B 927 PHE cc_start: 0.5566 (m-10) cc_final: 0.5215 (m-10) REVERT: B 1031 SER cc_start: 0.6452 (t) cc_final: 0.6111 (t) outliers start: 31 outliers final: 12 residues processed: 226 average time/residue: 1.2199 time to fit residues: 299.0303 Evaluate side-chains 222 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 207 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 313 GLU 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 Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 114 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 132 optimal weight: 0.0770 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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: 0.6779 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11459 Z= 0.281 Angle : 0.619 10.429 15546 Z= 0.322 Chirality : 0.045 0.234 1752 Planarity : 0.006 0.066 2032 Dihedral : 4.773 21.118 1578 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.60 % Allowed : 18.76 % Favored : 78.64 % 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: -0.26 (0.22), residues: 1429 helix: 0.74 (0.19), residues: 770 sheet: -1.07 (0.43), residues: 154 loop : -1.21 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 35 HIS 0.007 0.001 HIS A 167 PHE 0.024 0.002 PHE B 106 TYR 0.045 0.002 TYR B 874 ARG 0.009 0.001 ARG B 300 *********************** 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 244 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.7161 (mt0) cc_final: 0.6925 (mm110) REVERT: B 35 TRP cc_start: 0.7454 (OUTLIER) cc_final: 0.6884 (m-10) REVERT: B 359 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.8010 (pp) REVERT: B 525 TRP cc_start: 0.7599 (p90) cc_final: 0.7374 (p90) REVERT: B 602 PHE cc_start: 0.8161 (t80) cc_final: 0.7888 (t80) REVERT: B 715 TYR cc_start: 0.7976 (t80) cc_final: 0.7655 (t80) REVERT: B 852 LYS cc_start: 0.7109 (tttt) cc_final: 0.6841 (tttt) REVERT: B 867 THR cc_start: 0.8185 (OUTLIER) cc_final: 0.7966 (t) REVERT: B 927 PHE cc_start: 0.5539 (m-10) cc_final: 0.5284 (m-10) REVERT: B 1031 SER cc_start: 0.6476 (t) cc_final: 0.6146 (t) outliers start: 31 outliers final: 11 residues processed: 228 average time/residue: 1.3011 time to fit residues: 321.2880 Evaluate side-chains 221 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 207 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 501 LEU Chi-restraints excluded: chain B residue 608 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 867 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 136 optimal weight: 0.2980 chunk 85 optimal weight: 0.0770 chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 84 optimal weight: 0.0980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 434 HIS ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS B1125 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.2524 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= 0.219 Angle : 0.595 7.377 15546 Z= 0.307 Chirality : 0.043 0.175 1752 Planarity : 0.005 0.065 2032 Dihedral : 4.658 21.772 1578 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.18 % Allowed : 19.68 % Favored : 78.14 % 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: -0.10 (0.22), residues: 1429 helix: 0.89 (0.19), residues: 769 sheet: -1.02 (0.44), residues: 153 loop : -1.16 (0.27), residues: 507 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 0.024 0.002 PHE B 106 TYR 0.049 0.002 TYR B 874 ARG 0.007 0.001 ARG B1151 *********************** 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 232 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 206 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.7123 (mt0) cc_final: 0.6862 (mm110) REVERT: A 203 ARG cc_start: 0.7561 (ttm110) cc_final: 0.7308 (ttm-80) REVERT: A 206 ILE cc_start: 0.7784 (mp) cc_final: 0.7556 (tp) REVERT: B 35 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.6830 (m-10) REVERT: B 359 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7897 (pp) REVERT: B 525 TRP cc_start: 0.7570 (p90) cc_final: 0.7353 (p90) REVERT: B 602 PHE cc_start: 0.8148 (t80) cc_final: 0.7880 (t80) REVERT: B 715 TYR cc_start: 0.7871 (t80) cc_final: 0.7572 (t80) REVERT: B 852 LYS cc_start: 0.7082 (tttt) cc_final: 0.6830 (tttt) REVERT: B 867 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7973 (t) REVERT: B 927 PHE cc_start: 0.5481 (m-10) cc_final: 0.5228 (m-10) outliers start: 26 outliers final: 11 residues processed: 217 average time/residue: 1.2188 time to fit residues: 286.1348 Evaluate side-chains 219 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 205 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 684 HIS Chi-restraints excluded: chain B residue 796 ILE Chi-restraints excluded: chain B residue 867 THR Chi-restraints excluded: chain B residue 958 THR Chi-restraints excluded: chain B residue 973 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 67 optimal weight: 0.0040 chunk 12 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 124 optimal weight: 0.1980 chunk 131 optimal weight: 0.8980 overall best weight: 0.4992 ------------------------------------------------------------------------------- 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: 0.6771 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 0.048 11459 Z= 0.260 Angle : 0.615 6.807 15546 Z= 0.317 Chirality : 0.044 0.195 1752 Planarity : 0.005 0.048 2032 Dihedral : 4.705 22.540 1578 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.09 % Allowed : 20.69 % Favored : 77.22 % 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: -0.18 (0.22), residues: 1429 helix: 0.83 (0.19), residues: 768 sheet: -1.08 (0.43), residues: 154 loop : -1.19 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 232 HIS 0.006 0.001 HIS A 167 PHE 0.024 0.002 PHE B 106 TYR 0.050 0.002 TYR B 874 ARG 0.007 0.001 ARG B 837 *********************** 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 232 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 207 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 GLN cc_start: 0.7114 (mt0) cc_final: 0.6827 (mm110) REVERT: B 35 TRP cc_start: 0.7464 (OUTLIER) cc_final: 0.6841 (m-10) REVERT: B 525 TRP cc_start: 0.7596 (p90) cc_final: 0.7361 (p90) REVERT: B 602 PHE cc_start: 0.8165 (t80) cc_final: 0.7894 (t80) REVERT: B 715 TYR cc_start: 0.7953 (t80) cc_final: 0.7636 (t80) REVERT: B 852 LYS cc_start: 0.7076 (tttt) cc_final: 0.6827 (tttt) REVERT: B 927 PHE cc_start: 0.5598 (m-10) cc_final: 0.5358 (m-10) REVERT: B 979 MET cc_start: 0.6536 (mtt) cc_final: 0.6250 (mtt) REVERT: B 1166 LEU cc_start: 0.7771 (mp) cc_final: 0.7534 (mt) outliers start: 25 outliers final: 13 residues processed: 218 average time/residue: 1.3611 time to fit residues: 320.9609 Evaluate side-chains 220 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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 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 973 TYR Chi-restraints excluded: chain B residue 1023 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 131 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.0870 chunk 100 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 120 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11459 Z= 0.302 Angle : 0.652 8.346 15546 Z= 0.334 Chirality : 0.045 0.225 1752 Planarity : 0.005 0.050 2032 Dihedral : 4.827 23.270 1578 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.42 % Allowed : 21.78 % 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: -0.30 (0.22), residues: 1429 helix: 0.74 (0.19), residues: 767 sheet: -1.08 (0.43), residues: 154 loop : -1.26 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 232 HIS 0.008 0.001 HIS A 167 PHE 0.026 0.002 PHE B 106 TYR 0.053 0.003 TYR B 874 ARG 0.009 0.001 ARG B 837 *********************** 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 221 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 204 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.7412 (t80) cc_final: 0.6414 (t80) REVERT: A 92 ASN cc_start: 0.4880 (m110) cc_final: 0.4449 (m-40) REVERT: A 145 MET cc_start: 0.6083 (mmm) cc_final: 0.5835 (tpt) REVERT: A 179 GLN cc_start: 0.7147 (mt0) cc_final: 0.6855 (mm110) REVERT: B 35 TRP cc_start: 0.7488 (OUTLIER) cc_final: 0.6868 (m-10) REVERT: B 525 TRP cc_start: 0.7626 (p90) cc_final: 0.7412 (p90) REVERT: B 602 PHE cc_start: 0.8178 (t80) cc_final: 0.7898 (t80) REVERT: B 715 TYR cc_start: 0.7989 (t80) cc_final: 0.7632 (t80) REVERT: B 852 LYS cc_start: 0.7092 (tttt) cc_final: 0.6849 (tttt) REVERT: B 927 PHE cc_start: 0.5821 (m-10) cc_final: 0.5583 (m-10) REVERT: B 1166 LEU cc_start: 0.7785 (mp) cc_final: 0.7553 (mt) outliers start: 17 outliers final: 12 residues processed: 212 average time/residue: 1.2627 time to fit residues: 288.8809 Evaluate side-chains 212 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 199 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.7980 chunk 63 optimal weight: 0.2980 chunk 93 optimal weight: 0.0980 chunk 141 optimal weight: 0.0770 chunk 130 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 89 optimal weight: 0.0870 chunk 120 optimal weight: 0.9980 overall best weight: 0.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 545 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1026 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1125 HIS B1158 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11459 Z= 0.186 Angle : 0.603 10.135 15546 Z= 0.308 Chirality : 0.043 0.180 1752 Planarity : 0.005 0.075 2032 Dihedral : 4.599 22.153 1578 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.26 % Allowed : 22.11 % 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: 0.05 (0.23), residues: 1429 helix: 1.06 (0.19), residues: 766 sheet: -0.91 (0.43), residues: 153 loop : -1.18 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 946 HIS 0.005 0.001 HIS B 260 PHE 0.024 0.002 PHE B 106 TYR 0.049 0.002 TYR B 874 ARG 0.007 0.000 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 213 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 TYR cc_start: 0.7288 (t80) cc_final: 0.6279 (t80) REVERT: A 92 ASN cc_start: 0.4905 (m110) cc_final: 0.4481 (m-40) REVERT: A 145 MET cc_start: 0.6009 (mmm) cc_final: 0.5743 (tpt) REVERT: A 179 GLN cc_start: 0.7100 (mt0) cc_final: 0.6812 (mm110) REVERT: A 203 ARG cc_start: 0.7500 (ttm110) cc_final: 0.7297 (ttm-80) REVERT: B 35 TRP cc_start: 0.7384 (OUTLIER) cc_final: 0.6753 (m-10) REVERT: B 525 TRP cc_start: 0.7530 (p90) cc_final: 0.7304 (p90) REVERT: B 602 PHE cc_start: 0.8084 (t80) cc_final: 0.7828 (t80) REVERT: B 715 TYR cc_start: 0.7727 (t80) cc_final: 0.7441 (t80) REVERT: B 927 PHE cc_start: 0.5561 (m-10) cc_final: 0.5334 (m-10) REVERT: B 977 TRP cc_start: 0.5035 (t60) cc_final: 0.4444 (t60) REVERT: B 979 MET cc_start: 0.6190 (mtt) cc_final: 0.5967 (mtt) REVERT: B 1166 LEU cc_start: 0.7701 (mp) cc_final: 0.7473 (mt) outliers start: 15 outliers final: 11 residues processed: 204 average time/residue: 1.3412 time to fit residues: 294.3928 Evaluate side-chains 208 residues out of total 1194 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 196 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER 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 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 998 THR Chi-restraints excluded: chain B residue 1023 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: 4.9990 chunk 16 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4363 r_free = 0.4363 target = 0.182536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.168472 restraints weight = 15208.516| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 1.72 r_work: 0.4124 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3994 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11459 Z= 0.346 Angle : 0.694 11.828 15546 Z= 0.351 Chirality : 0.047 0.236 1752 Planarity : 0.006 0.105 2032 Dihedral : 4.885 23.818 1578 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.34 % Allowed : 22.45 % Favored : 76.21 % 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: -0.26 (0.22), residues: 1429 helix: 0.79 (0.19), residues: 762 sheet: -1.03 (0.43), residues: 154 loop : -1.29 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 232 HIS 0.009 0.002 HIS A 167 PHE 0.026 0.002 PHE B 106 TYR 0.056 0.003 TYR B 874 ARG 0.011 0.001 ARG B 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5266.02 seconds wall clock time: 92 minutes 17.48 seconds (5537.48 seconds total)