Starting phenix.real_space_refine on Mon Mar 11 09:00:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/03_2024/7rqs_24635.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/03_2024/7rqs_24635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/03_2024/7rqs_24635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/03_2024/7rqs_24635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/03_2024/7rqs_24635.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rqs_24635/03_2024/7rqs_24635.pdb" } resolution = 3.57 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= 0.002 sd= 0.028 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: 5 Type Number sf(0) Gaussians Mg 1 5.21 5 S 48 5.16 5 C 4898 2.51 5 N 1349 2.21 5 O 1496 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 879": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7792 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1075, 7792 Unusual residues: {' MG': 1} Classifications: {'peptide': 1074, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 38, 'TRANS': 1035, None: 1} Not linked: pdbres="GLN A1121 " pdbres=" MG A1201 " Chain breaks: 8 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 860 Unresolved non-hydrogen angles: 1087 Unresolved non-hydrogen dihedrals: 768 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 3, 'TYR:plan': 20, 'ASN:plan1': 4, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 15, 'GLU:plan': 21, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 522 Time building chain proxies: 4.63, per 1000 atoms: 0.59 Number of scatterers: 7792 At special positions: 0 Unit cell: (81.024, 101.28, 108.454, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 48 16.00 Mg 1 11.99 O 1496 8.00 N 1349 7.00 C 4898 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: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 9 sheets defined 38.2% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 22 through 34 removed outlier: 3.546A pdb=" N LEU A 32 " --> pdb=" O ARG A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.657A pdb=" N SER A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 229 through 234 removed outlier: 3.596A pdb=" N THR A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 273 Processing helix chain 'A' and resid 295 through 305 removed outlier: 4.155A pdb=" N ALA A 301 " --> pdb=" O PHE A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 315 through 325 removed outlier: 3.704A pdb=" N MET A 325 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 346 through 356 Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 409 through 413 removed outlier: 5.610A pdb=" N SER A 413 " --> pdb=" O GLU A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 434 removed outlier: 3.531A pdb=" N LEU A 433 " --> pdb=" O PRO A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 460 Processing helix chain 'A' and resid 475 through 481 Processing helix chain 'A' and resid 496 through 503 removed outlier: 3.523A pdb=" N GLY A 503 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 521 removed outlier: 4.438A pdb=" N LEU A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 645 through 662 removed outlier: 3.981A pdb=" N PHE A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU A 650 " --> pdb=" O ASP A 646 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ALA A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET A 652 " --> pdb=" O MET A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 671 removed outlier: 3.872A pdb=" N ALA A 669 " --> pdb=" O ASP A 666 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU A 671 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 692 Processing helix chain 'A' and resid 699 through 720 Processing helix chain 'A' and resid 753 through 759 Processing helix chain 'A' and resid 802 through 807 Processing helix chain 'A' and resid 821 through 826 removed outlier: 3.517A pdb=" N CYS A 826 " --> pdb=" O HIS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 882 Processing helix chain 'A' and resid 884 through 896 removed outlier: 3.611A pdb=" N ILE A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 921 Processing helix chain 'A' and resid 931 through 935 Processing helix chain 'A' and resid 958 through 969 removed outlier: 3.864A pdb=" N ARG A 962 " --> pdb=" O GLY A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 991 removed outlier: 3.812A pdb=" N GLU A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLU A 989 " --> pdb=" O VAL A 985 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1018 removed outlier: 4.259A pdb=" N ALA A1001 " --> pdb=" O GLU A 997 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU A1008 " --> pdb=" O ASP A1004 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A1017 " --> pdb=" O LEU A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1068 removed outlier: 3.563A pdb=" N ASP A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 4.030A pdb=" N VAL A1106 " --> pdb=" O PHE A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1117 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 13 removed outlier: 6.604A pdb=" N GLN A 60 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 221 removed outlier: 4.018A pdb=" N MET A 218 " --> pdb=" O VAL A 195 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 195 " --> pdb=" O MET A 218 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 220 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 155 " --> pdb=" O PHE A 192 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 142 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLU A 127 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 113 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ILE A 109 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG A 133 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP A 107 " --> pdb=" O ARG A 133 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N TRP A 135 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG A 105 " --> pdb=" O TRP A 135 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 110 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 9.155A pdb=" N LEU A 262 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SER A 168 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 125 removed outlier: 3.653A pdb=" N ALA A 125 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 393 through 400 removed outlier: 5.527A pdb=" N LEU A 393 " --> pdb=" O TYR A 385 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR A 385 " --> pdb=" O LEU A 393 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY A 395 " --> pdb=" O ARG A 383 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 383 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N PHE A 415 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN A 382 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG A 417 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N TRP A 485 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 526 through 530 removed outlier: 4.655A pdb=" N LEU A 618 " --> pdb=" O THR A 528 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 557 through 560 removed outlier: 6.371A pdb=" N GLY A 558 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG A 622 " --> pdb=" O GLN A 582 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 627 through 628 removed outlier: 4.384A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 730 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE A 812 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE A 732 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N PHE A 814 " --> pdb=" O ILE A 732 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N CYS A 734 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N CYS A 811 " --> pdb=" O ARG A 749 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG A 749 " --> pdb=" O CYS A 811 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL A 748 " --> pdb=" O VAL A 775 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 628 removed outlier: 4.384A pdb=" N MET A 627 " --> pdb=" O ILE A 730 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 730 " --> pdb=" O MET A 627 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL A 748 " --> pdb=" O VAL A 775 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 939 through 940 removed outlier: 6.396A pdb=" N PHE A 939 " --> pdb=" O TYR A 951 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 323 hydrogen bonds defined for protein. 924 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: 3.28 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2101 1.33 - 1.45: 1219 1.45 - 1.57: 4516 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 7910 Sorted by residual: bond pdb=" C ARG A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.332 1.367 -0.035 1.32e-02 5.74e+03 7.05e+00 bond pdb=" N VAL A 100 " pdb=" CA VAL A 100 " ideal model delta sigma weight residual 1.461 1.490 -0.030 1.19e-02 7.06e+03 6.27e+00 bond pdb=" N ARG A 98 " pdb=" CA ARG A 98 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.70e-02 3.46e+03 5.23e+00 bond pdb=" N ARG A 103 " pdb=" CA ARG A 103 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.33e-02 5.65e+03 4.77e+00 bond pdb=" N ASP A 101 " pdb=" CA ASP A 101 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.76e-02 3.23e+03 3.00e+00 ... (remaining 7905 not shown) Histogram of bond angle deviations from ideal: 98.88 - 105.90: 149 105.90 - 112.91: 4365 112.91 - 119.93: 2525 119.93 - 126.95: 3628 126.95 - 133.96: 68 Bond angle restraints: 10735 Sorted by residual: angle pdb=" N PRO A 99 " pdb=" CA PRO A 99 " pdb=" CB PRO A 99 " ideal model delta sigma weight residual 103.34 106.68 -3.34 9.30e-01 1.16e+00 1.29e+01 angle pdb=" CA VAL A 100 " pdb=" C VAL A 100 " pdb=" O VAL A 100 " ideal model delta sigma weight residual 120.95 117.68 3.27 1.04e+00 9.25e-01 9.86e+00 angle pdb=" N GLN A 570 " pdb=" CA GLN A 570 " pdb=" CB GLN A 570 " ideal model delta sigma weight residual 110.16 114.68 -4.52 1.48e+00 4.57e-01 9.34e+00 angle pdb=" N PRO A 97 " pdb=" CA PRO A 97 " pdb=" C PRO A 97 " ideal model delta sigma weight residual 112.47 118.50 -6.03 2.06e+00 2.36e-01 8.57e+00 angle pdb=" CA ILE A 96 " pdb=" C ILE A 96 " pdb=" N PRO A 97 " ideal model delta sigma weight residual 119.42 122.14 -2.72 9.30e-01 1.16e+00 8.55e+00 ... (remaining 10730 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4328 17.20 - 34.40: 377 34.40 - 51.59: 80 51.59 - 68.79: 9 68.79 - 85.99: 3 Dihedral angle restraints: 4797 sinusoidal: 1675 harmonic: 3122 Sorted by residual: dihedral pdb=" CA GLU A 117 " pdb=" C GLU A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA ASP A 174 " pdb=" CB ASP A 174 " pdb=" CG ASP A 174 " pdb=" OD1 ASP A 174 " ideal model delta sinusoidal sigma weight residual -30.00 -82.65 52.65 1 2.00e+01 2.50e-03 9.44e+00 dihedral pdb=" N VAL A 100 " pdb=" CA VAL A 100 " pdb=" CB VAL A 100 " pdb=" CG1 VAL A 100 " ideal model delta sinusoidal sigma weight residual 60.00 8.22 51.78 3 1.50e+01 4.44e-03 9.05e+00 ... (remaining 4794 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 928 0.040 - 0.080: 247 0.080 - 0.120: 89 0.120 - 0.161: 6 0.161 - 0.201: 3 Chirality restraints: 1273 Sorted by residual: chirality pdb=" CA PRO A 97 " pdb=" N PRO A 97 " pdb=" C PRO A 97 " pdb=" CB PRO A 97 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB THR A 463 " pdb=" CA THR A 463 " pdb=" OG1 THR A 463 " pdb=" CG2 THR A 463 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CB VAL A 100 " pdb=" CA VAL A 100 " pdb=" CG1 VAL A 100 " pdb=" CG2 VAL A 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 1270 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 845 " 0.066 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO A 846 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO A 846 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 846 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 850 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.64e+00 pdb=" N PRO A 851 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 851 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 851 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 346 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 347 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 347 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 347 " 0.022 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 90 2.65 - 3.21: 7505 3.21 - 3.78: 11846 3.78 - 4.34: 15587 4.34 - 4.90: 25512 Nonbonded interactions: 60540 Sorted by model distance: nonbonded pdb=" OD1 ASP A 832 " pdb="MG MG A1201 " model vdw 2.088 2.170 nonbonded pdb=" O SER A 682 " pdb=" NZ LYS A 688 " model vdw 2.213 2.520 nonbonded pdb=" O ALA A 432 " pdb=" OG1 THR A 448 " model vdw 2.255 2.440 nonbonded pdb=" NH2 ARG A 506 " pdb=" O ASP A 612 " model vdw 2.257 2.520 nonbonded pdb=" O GLY A 503 " pdb=" NH1 ARG A 506 " model vdw 2.267 2.520 ... (remaining 60535 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.850 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: 0.000 Extract box with map and model: 31.060 Check model and map are aligned: 0.230 Set scattering table: 0.070 Process input model: 25.310 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 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 : 0.002 0.039 7910 Z= 0.172 Angle : 0.544 7.784 10735 Z= 0.301 Chirality : 0.041 0.201 1273 Planarity : 0.004 0.099 1400 Dihedral : 13.383 85.988 2757 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.26 % Allowed : 0.00 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 1057 helix: 1.27 (0.29), residues: 354 sheet: -1.41 (0.44), residues: 142 loop : -1.67 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.002 0.001 HIS A 710 PHE 0.010 0.001 PHE A 471 TYR 0.023 0.001 TYR A 799 ARG 0.007 0.000 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 0.841 Fit side-chains revert: symmetry clash REVERT: A 153 CYS cc_start: 0.6585 (t) cc_final: 0.6292 (t) REVERT: A 281 LEU cc_start: 0.7121 (mp) cc_final: 0.6820 (mp) REVERT: A 282 LEU cc_start: 0.7430 (mt) cc_final: 0.7166 (mt) REVERT: A 328 GLU cc_start: 0.6633 (mp0) cc_final: 0.6331 (mp0) REVERT: A 355 MET cc_start: 0.4699 (tpt) cc_final: 0.4496 (tpt) REVERT: A 424 ASP cc_start: 0.7269 (p0) cc_final: 0.7033 (p0) REVERT: A 487 PHE cc_start: 0.7627 (t80) cc_final: 0.7414 (t80) REVERT: A 879 TYR cc_start: 0.7266 (t80) cc_final: 0.6828 (t80) REVERT: A 883 ASP cc_start: 0.7864 (t70) cc_final: 0.7378 (t0) REVERT: A 897 ASP cc_start: 0.7638 (m-30) cc_final: 0.7179 (m-30) REVERT: A 907 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7538 (mtmt) outliers start: 2 outliers final: 1 residues processed: 156 average time/residue: 0.1950 time to fit residues: 41.2569 Evaluate side-chains 137 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7910 Z= 0.305 Angle : 0.599 8.568 10735 Z= 0.317 Chirality : 0.044 0.180 1273 Planarity : 0.005 0.062 1400 Dihedral : 4.589 31.851 1125 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 1.58 % Allowed : 10.03 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.26), residues: 1057 helix: 0.56 (0.27), residues: 371 sheet: -1.30 (0.44), residues: 144 loop : -1.75 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 485 HIS 0.007 0.001 HIS A 411 PHE 0.022 0.002 PHE A 471 TYR 0.015 0.002 TYR A 385 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 152 time to evaluate : 0.856 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7542 (mtmt) REVERT: A 153 CYS cc_start: 0.6517 (t) cc_final: 0.6192 (t) REVERT: A 239 LEU cc_start: 0.8092 (mt) cc_final: 0.7868 (mt) REVERT: A 282 LEU cc_start: 0.7560 (mt) cc_final: 0.7271 (mt) REVERT: A 346 ASP cc_start: 0.6560 (p0) cc_final: 0.6322 (p0) REVERT: A 355 MET cc_start: 0.4768 (tpt) cc_final: 0.4502 (tpt) REVERT: A 424 ASP cc_start: 0.7368 (p0) cc_final: 0.7065 (p0) REVERT: A 482 ASN cc_start: 0.7690 (m-40) cc_final: 0.7114 (m110) REVERT: A 487 PHE cc_start: 0.7780 (t80) cc_final: 0.7568 (t80) REVERT: A 762 GLN cc_start: 0.7993 (mp10) cc_final: 0.7655 (mp10) REVERT: A 880 MET cc_start: 0.7328 (tpp) cc_final: 0.6492 (mpp) REVERT: A 883 ASP cc_start: 0.7984 (t70) cc_final: 0.7511 (t0) REVERT: A 923 LYS cc_start: 0.7732 (mtmm) cc_final: 0.7432 (mtmm) REVERT: A 957 PHE cc_start: 0.5327 (p90) cc_final: 0.3440 (p90) outliers start: 12 outliers final: 6 residues processed: 158 average time/residue: 0.1873 time to fit residues: 40.6897 Evaluate side-chains 153 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 147 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 924 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7910 Z= 0.222 Angle : 0.535 10.201 10735 Z= 0.281 Chirality : 0.042 0.163 1273 Planarity : 0.004 0.051 1400 Dihedral : 4.339 24.591 1125 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 1.06 % Allowed : 15.57 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1057 helix: 0.78 (0.28), residues: 367 sheet: -1.33 (0.43), residues: 145 loop : -1.69 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 485 HIS 0.006 0.001 HIS A 411 PHE 0.019 0.001 PHE A 471 TYR 0.020 0.001 TYR A 879 ARG 0.002 0.000 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 147 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 153 CYS cc_start: 0.6454 (t) cc_final: 0.6135 (t) REVERT: A 282 LEU cc_start: 0.7549 (mt) cc_final: 0.7302 (mt) REVERT: A 328 GLU cc_start: 0.6702 (mp0) cc_final: 0.6333 (mp0) REVERT: A 346 ASP cc_start: 0.6480 (p0) cc_final: 0.6185 (p0) REVERT: A 355 MET cc_start: 0.4727 (tpt) cc_final: 0.4463 (tpt) REVERT: A 424 ASP cc_start: 0.7315 (p0) cc_final: 0.6994 (p0) REVERT: A 478 GLN cc_start: 0.7619 (tt0) cc_final: 0.7092 (tt0) REVERT: A 487 PHE cc_start: 0.7728 (t80) cc_final: 0.7471 (t80) REVERT: A 663 MET cc_start: 0.8307 (ptm) cc_final: 0.8026 (ttp) REVERT: A 883 ASP cc_start: 0.7994 (t70) cc_final: 0.7483 (t0) REVERT: A 907 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7623 (mtmt) REVERT: A 923 LYS cc_start: 0.7726 (mtmm) cc_final: 0.7383 (mtmm) REVERT: A 957 PHE cc_start: 0.5557 (p90) cc_final: 0.3629 (p90) outliers start: 8 outliers final: 4 residues processed: 150 average time/residue: 0.1837 time to fit residues: 38.3949 Evaluate side-chains 150 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 924 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7910 Z= 0.237 Angle : 0.541 8.373 10735 Z= 0.284 Chirality : 0.042 0.161 1273 Planarity : 0.004 0.051 1400 Dihedral : 4.336 18.962 1124 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.80 % Favored : 91.11 % Rotamer: Outliers : 1.98 % Allowed : 17.55 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.26), residues: 1057 helix: 0.79 (0.28), residues: 373 sheet: -1.38 (0.43), residues: 145 loop : -1.73 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.006 0.001 HIS A 411 PHE 0.021 0.001 PHE A 471 TYR 0.021 0.002 TYR A 879 ARG 0.001 0.000 ARG A 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 153 CYS cc_start: 0.6413 (t) cc_final: 0.6123 (t) REVERT: A 223 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7795 (m) REVERT: A 239 LEU cc_start: 0.8005 (mt) cc_final: 0.7782 (mt) REVERT: A 282 LEU cc_start: 0.7555 (mt) cc_final: 0.7308 (mt) REVERT: A 328 GLU cc_start: 0.6735 (mp0) cc_final: 0.6360 (mp0) REVERT: A 346 ASP cc_start: 0.6467 (p0) cc_final: 0.6194 (p0) REVERT: A 355 MET cc_start: 0.4698 (tpt) cc_final: 0.4431 (tpt) REVERT: A 424 ASP cc_start: 0.7332 (p0) cc_final: 0.7069 (p0) REVERT: A 487 PHE cc_start: 0.7754 (t80) cc_final: 0.7527 (t80) REVERT: A 663 MET cc_start: 0.8309 (ptm) cc_final: 0.8046 (ttp) REVERT: A 724 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8123 (tp) REVERT: A 762 GLN cc_start: 0.8394 (mp10) cc_final: 0.7836 (mp10) REVERT: A 883 ASP cc_start: 0.7998 (t70) cc_final: 0.7505 (t0) REVERT: A 907 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7634 (mtmt) REVERT: A 923 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7404 (mtmm) REVERT: A 935 LYS cc_start: 0.8242 (mmmm) cc_final: 0.7999 (mmmm) REVERT: A 957 PHE cc_start: 0.5713 (p90) cc_final: 0.3821 (p90) outliers start: 15 outliers final: 7 residues processed: 164 average time/residue: 0.1800 time to fit residues: 41.0516 Evaluate side-chains 164 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 924 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 88 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7910 Z= 0.182 Angle : 0.517 8.477 10735 Z= 0.270 Chirality : 0.041 0.153 1273 Planarity : 0.004 0.061 1400 Dihedral : 4.166 18.210 1124 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 1.98 % Allowed : 19.79 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.26), residues: 1057 helix: 0.89 (0.28), residues: 370 sheet: -1.37 (0.43), residues: 145 loop : -1.69 (0.25), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 623 HIS 0.010 0.001 HIS A 411 PHE 0.020 0.001 PHE A 957 TYR 0.021 0.001 TYR A 879 ARG 0.002 0.000 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 CYS cc_start: 0.6436 (t) cc_final: 0.6167 (t) REVERT: A 239 LEU cc_start: 0.7980 (mt) cc_final: 0.7757 (mt) REVERT: A 282 LEU cc_start: 0.7532 (mt) cc_final: 0.7327 (mt) REVERT: A 355 MET cc_start: 0.4677 (tpt) cc_final: 0.4437 (tpt) REVERT: A 424 ASP cc_start: 0.7308 (p0) cc_final: 0.7054 (p0) REVERT: A 487 PHE cc_start: 0.7728 (t80) cc_final: 0.7482 (t80) REVERT: A 663 MET cc_start: 0.8291 (ptm) cc_final: 0.8053 (ttp) REVERT: A 724 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.8086 (tp) REVERT: A 762 GLN cc_start: 0.8347 (mp10) cc_final: 0.7831 (mp10) REVERT: A 880 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6263 (mpp) REVERT: A 883 ASP cc_start: 0.8005 (t70) cc_final: 0.7485 (t0) REVERT: A 923 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7401 (mtmm) REVERT: A 935 LYS cc_start: 0.8214 (mmmm) cc_final: 0.8006 (mmmm) REVERT: A 957 PHE cc_start: 0.5689 (p90) cc_final: 0.3740 (p90) outliers start: 15 outliers final: 6 residues processed: 158 average time/residue: 0.1859 time to fit residues: 41.1821 Evaluate side-chains 157 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 149 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 959 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 99 optimal weight: 30.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7910 Z= 0.241 Angle : 0.564 12.505 10735 Z= 0.292 Chirality : 0.042 0.191 1273 Planarity : 0.004 0.049 1400 Dihedral : 4.339 18.466 1124 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.99 % Favored : 90.92 % Rotamer: Outliers : 2.51 % Allowed : 20.84 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1057 helix: 0.85 (0.28), residues: 374 sheet: -1.37 (0.43), residues: 145 loop : -1.69 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 485 HIS 0.009 0.001 HIS A 411 PHE 0.022 0.002 PHE A 471 TYR 0.023 0.001 TYR A 879 ARG 0.001 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 LEU cc_start: 0.7992 (mt) cc_final: 0.7730 (mt) REVERT: A 282 LEU cc_start: 0.7548 (mt) cc_final: 0.7332 (mt) REVERT: A 328 GLU cc_start: 0.6724 (mp0) cc_final: 0.6321 (mp0) REVERT: A 355 MET cc_start: 0.4648 (tpt) cc_final: 0.4402 (tpt) REVERT: A 424 ASP cc_start: 0.7322 (p0) cc_final: 0.7065 (p0) REVERT: A 478 GLN cc_start: 0.7586 (tt0) cc_final: 0.7156 (tt0) REVERT: A 487 PHE cc_start: 0.7735 (t80) cc_final: 0.7513 (t80) REVERT: A 663 MET cc_start: 0.8304 (ptm) cc_final: 0.8069 (ttp) REVERT: A 724 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8028 (tp) REVERT: A 762 GLN cc_start: 0.8355 (mp10) cc_final: 0.7851 (mp10) REVERT: A 869 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6376 (mt) REVERT: A 880 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6277 (mpp) REVERT: A 883 ASP cc_start: 0.8028 (t70) cc_final: 0.7511 (t0) REVERT: A 897 ASP cc_start: 0.7837 (m-30) cc_final: 0.7324 (m-30) REVERT: A 923 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7408 (mtmm) REVERT: A 935 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7988 (mmmm) REVERT: A 957 PHE cc_start: 0.5719 (p90) cc_final: 0.3742 (p90) outliers start: 19 outliers final: 10 residues processed: 159 average time/residue: 0.1865 time to fit residues: 41.5348 Evaluate side-chains 164 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 959 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 75 optimal weight: 0.0970 chunk 87 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7910 Z= 0.199 Angle : 0.528 8.837 10735 Z= 0.276 Chirality : 0.041 0.154 1273 Planarity : 0.004 0.065 1400 Dihedral : 4.191 18.126 1124 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.70 % Favored : 91.20 % Rotamer: Outliers : 2.24 % Allowed : 21.37 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.26), residues: 1057 helix: 0.95 (0.28), residues: 370 sheet: -1.31 (0.43), residues: 145 loop : -1.68 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 623 HIS 0.008 0.001 HIS A 411 PHE 0.019 0.001 PHE A 471 TYR 0.022 0.001 TYR A 879 ARG 0.001 0.000 ARG A 766 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 LEU cc_start: 0.7979 (mt) cc_final: 0.7719 (mt) REVERT: A 282 LEU cc_start: 0.7549 (mt) cc_final: 0.7339 (mt) REVERT: A 328 GLU cc_start: 0.6727 (mp0) cc_final: 0.6298 (mp0) REVERT: A 355 MET cc_start: 0.4636 (tpt) cc_final: 0.4381 (tpt) REVERT: A 424 ASP cc_start: 0.7296 (p0) cc_final: 0.7037 (p0) REVERT: A 478 GLN cc_start: 0.7571 (tt0) cc_final: 0.7125 (tt0) REVERT: A 487 PHE cc_start: 0.7719 (t80) cc_final: 0.7503 (t80) REVERT: A 724 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.8017 (tp) REVERT: A 762 GLN cc_start: 0.8314 (mp10) cc_final: 0.7888 (mp10) REVERT: A 880 MET cc_start: 0.7030 (OUTLIER) cc_final: 0.6216 (mpp) REVERT: A 883 ASP cc_start: 0.8014 (t70) cc_final: 0.7477 (t0) REVERT: A 923 LYS cc_start: 0.7688 (mtmm) cc_final: 0.7402 (mtmm) REVERT: A 935 LYS cc_start: 0.8167 (mmmm) cc_final: 0.7964 (mmmm) REVERT: A 957 PHE cc_start: 0.5710 (p90) cc_final: 0.3721 (p90) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 0.1862 time to fit residues: 41.5144 Evaluate side-chains 166 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 152 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 924 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7910 Z= 0.325 Angle : 0.603 9.039 10735 Z= 0.318 Chirality : 0.044 0.160 1273 Planarity : 0.004 0.055 1400 Dihedral : 4.641 19.684 1124 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.74 % Favored : 90.16 % Rotamer: Outliers : 2.77 % Allowed : 21.11 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.26), residues: 1057 helix: 0.66 (0.28), residues: 374 sheet: -1.34 (0.42), residues: 150 loop : -1.81 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 485 HIS 0.009 0.001 HIS A 411 PHE 0.026 0.002 PHE A 471 TYR 0.027 0.002 TYR A 879 ARG 0.002 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 158 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 LEU cc_start: 0.8002 (mt) cc_final: 0.7755 (mt) REVERT: A 282 LEU cc_start: 0.7558 (mt) cc_final: 0.7349 (mt) REVERT: A 328 GLU cc_start: 0.6753 (mp0) cc_final: 0.6313 (mp0) REVERT: A 355 MET cc_start: 0.4608 (tpt) cc_final: 0.4358 (tpt) REVERT: A 424 ASP cc_start: 0.7309 (p0) cc_final: 0.7023 (p0) REVERT: A 487 PHE cc_start: 0.7765 (t80) cc_final: 0.7539 (t80) REVERT: A 664 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8104 (mt) REVERT: A 724 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8080 (tp) REVERT: A 762 GLN cc_start: 0.8365 (mp10) cc_final: 0.7831 (mp10) REVERT: A 869 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6447 (mt) REVERT: A 880 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6279 (mpp) REVERT: A 883 ASP cc_start: 0.8033 (t70) cc_final: 0.7512 (t0) REVERT: A 897 ASP cc_start: 0.7839 (m-30) cc_final: 0.7318 (m-30) REVERT: A 907 LYS cc_start: 0.8049 (mtmt) cc_final: 0.7640 (mtmt) REVERT: A 923 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7450 (mtmm) REVERT: A 957 PHE cc_start: 0.5753 (p90) cc_final: 0.3880 (p90) outliers start: 21 outliers final: 16 residues processed: 166 average time/residue: 0.1960 time to fit residues: 44.9190 Evaluate side-chains 179 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 924 THR Chi-restraints excluded: chain A residue 959 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 0.0970 chunk 29 optimal weight: 0.8980 chunk 86 optimal weight: 0.1980 chunk 95 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN A 653 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7910 Z= 0.169 Angle : 0.538 12.233 10735 Z= 0.275 Chirality : 0.041 0.195 1273 Planarity : 0.004 0.054 1400 Dihedral : 4.160 19.268 1124 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.04 % Favored : 91.86 % Rotamer: Outliers : 1.98 % Allowed : 22.82 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.26), residues: 1057 helix: 0.97 (0.28), residues: 371 sheet: -1.27 (0.43), residues: 147 loop : -1.70 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.021 0.001 PHE A 957 TYR 0.022 0.001 TYR A 879 ARG 0.002 0.000 ARG A 383 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 LEU cc_start: 0.7985 (mt) cc_final: 0.7755 (mt) REVERT: A 328 GLU cc_start: 0.6728 (mp0) cc_final: 0.6294 (mp0) REVERT: A 355 MET cc_start: 0.4572 (tpt) cc_final: 0.4324 (tpt) REVERT: A 424 ASP cc_start: 0.7205 (p0) cc_final: 0.6940 (p0) REVERT: A 478 GLN cc_start: 0.7557 (tt0) cc_final: 0.7105 (tt0) REVERT: A 487 PHE cc_start: 0.7708 (t80) cc_final: 0.7461 (t80) REVERT: A 688 LYS cc_start: 0.7249 (mptt) cc_final: 0.7041 (mttt) REVERT: A 724 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7983 (tp) REVERT: A 762 GLN cc_start: 0.8291 (mp10) cc_final: 0.7882 (mp10) REVERT: A 869 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6280 (mt) REVERT: A 880 MET cc_start: 0.7005 (OUTLIER) cc_final: 0.6160 (mpp) REVERT: A 883 ASP cc_start: 0.8015 (t70) cc_final: 0.7462 (t0) REVERT: A 923 LYS cc_start: 0.7674 (mtmm) cc_final: 0.7381 (mtmm) REVERT: A 957 PHE cc_start: 0.5685 (p90) cc_final: 0.3606 (p90) outliers start: 15 outliers final: 11 residues processed: 158 average time/residue: 0.1981 time to fit residues: 43.2479 Evaluate side-chains 165 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 151 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 880 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 98 optimal weight: 0.0040 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN A 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7910 Z= 0.236 Angle : 0.580 12.094 10735 Z= 0.298 Chirality : 0.042 0.179 1273 Planarity : 0.004 0.051 1400 Dihedral : 4.306 19.140 1124 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.27 % Favored : 90.63 % Rotamer: Outliers : 1.98 % Allowed : 22.69 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1057 helix: 0.88 (0.28), residues: 376 sheet: -1.24 (0.43), residues: 145 loop : -1.78 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.022 0.002 PHE A 471 TYR 0.027 0.002 TYR A 879 ARG 0.004 0.000 ARG A 605 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 LEU cc_start: 0.8017 (mt) cc_final: 0.7739 (mt) REVERT: A 328 GLU cc_start: 0.6749 (mp0) cc_final: 0.6304 (mp0) REVERT: A 355 MET cc_start: 0.4564 (tpt) cc_final: 0.4324 (tpt) REVERT: A 424 ASP cc_start: 0.7218 (p0) cc_final: 0.6965 (p0) REVERT: A 478 GLN cc_start: 0.7586 (tt0) cc_final: 0.7133 (tt0) REVERT: A 487 PHE cc_start: 0.7739 (t80) cc_final: 0.7509 (t80) REVERT: A 664 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8146 (mt) REVERT: A 724 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.8041 (tp) REVERT: A 762 GLN cc_start: 0.8333 (mp10) cc_final: 0.7898 (mp10) REVERT: A 869 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6316 (mt) REVERT: A 880 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6204 (mpp) REVERT: A 883 ASP cc_start: 0.8039 (t70) cc_final: 0.7502 (t0) REVERT: A 897 ASP cc_start: 0.7827 (m-30) cc_final: 0.7302 (m-30) REVERT: A 923 LYS cc_start: 0.7696 (mtmm) cc_final: 0.7407 (mtmm) REVERT: A 957 PHE cc_start: 0.5702 (p90) cc_final: 0.3773 (p90) outliers start: 15 outliers final: 10 residues processed: 151 average time/residue: 0.1886 time to fit residues: 39.4643 Evaluate side-chains 157 residues out of total 950 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 497 ASP Chi-restraints excluded: chain A residue 570 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 646 ASP Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 880 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.174057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148122 restraints weight = 10744.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152070 restraints weight = 6094.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154616 restraints weight = 4098.946| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7910 Z= 0.329 Angle : 0.628 11.859 10735 Z= 0.328 Chirality : 0.045 0.176 1273 Planarity : 0.004 0.059 1400 Dihedral : 4.712 19.880 1124 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.60 % Favored : 89.31 % Rotamer: Outliers : 2.24 % Allowed : 22.43 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.26), residues: 1057 helix: 0.66 (0.28), residues: 373 sheet: -1.31 (0.43), residues: 145 loop : -1.89 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 485 HIS 0.010 0.001 HIS A 411 PHE 0.027 0.002 PHE A 471 TYR 0.031 0.002 TYR A 879 ARG 0.004 0.000 ARG A 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2999.93 seconds wall clock time: 54 minutes 48.96 seconds (3288.96 seconds total)