Starting phenix.real_space_refine on Sat Dec 28 04:56:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqs_24635/12_2024/7rqs_24635.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqs_24635/12_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/cci-nas-00/data/ceres_data/7rqs_24635/12_2024/7rqs_24635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqs_24635/12_2024/7rqs_24635.map" model { file = "/net/cci-nas-00/data/ceres_data/7rqs_24635/12_2024/7rqs_24635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqs_24635/12_2024/7rqs_24635.cif" } 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. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 7792 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1074, 7791 Classifications: {'peptide': 1074} Incomplete info: {'truncation_to_alanine': 192} Link IDs: {'PTRANS': 38, 'TRANS': 1035} 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 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.09, per 1000 atoms: 0.78 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.0 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: 1.06 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: 3.22 Time building geometry restraints manager: 2.39 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: 0.00 - 1.56: 10505 1.56 - 3.11: 187 3.11 - 4.67: 37 4.67 - 6.23: 4 6.23 - 7.78: 2 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 3.120 nonbonded pdb=" O ALA A 432 " pdb=" OG1 THR A 448 " model vdw 2.255 3.040 nonbonded pdb=" NH2 ARG A 506 " pdb=" O ASP A 612 " model vdw 2.257 3.120 nonbonded pdb=" O GLY A 503 " pdb=" NH1 ARG A 506 " model vdw 2.267 3.120 ... (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: 7.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.510 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.720 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.450 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.861 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: 0.2080 time to fit residues: 44.2209 Evaluate side-chains 137 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.9990 chunk 83 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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** A 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6697 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7910 Z= 0.296 Angle : 0.597 8.466 10735 Z= 0.317 Chirality : 0.044 0.182 1273 Planarity : 0.005 0.062 1400 Dihedral : 4.561 33.220 1125 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.72 % Allowed : 9.76 % Favored : 88.52 % 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 (0.25), residues: 1057 helix: 0.55 (0.27), residues: 365 sheet: -1.40 (0.45), residues: 139 loop : -1.73 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 485 HIS 0.007 0.001 HIS A 411 PHE 0.021 0.002 PHE A 471 TYR 0.014 0.002 TYR A 747 ARG 0.004 0.001 ARG A 453 *********************** 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 to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7888 (mtmt) cc_final: 0.7527 (mtmt) REVERT: A 153 CYS cc_start: 0.6587 (t) cc_final: 0.6289 (t) REVERT: A 239 LEU cc_start: 0.8122 (mt) cc_final: 0.7890 (mt) REVERT: A 282 LEU cc_start: 0.7550 (mt) cc_final: 0.7252 (mt) REVERT: A 346 ASP cc_start: 0.6579 (p0) cc_final: 0.6338 (p0) REVERT: A 355 MET cc_start: 0.4792 (tpt) cc_final: 0.4535 (tpt) REVERT: A 424 ASP cc_start: 0.7333 (p0) cc_final: 0.7045 (p0) REVERT: A 662 ASN cc_start: 0.7452 (m-40) cc_final: 0.7246 (m-40) REVERT: A 688 LYS cc_start: 0.7444 (mptt) cc_final: 0.6783 (mptt) REVERT: A 870 GLU cc_start: 0.6837 (tm-30) cc_final: 0.6631 (tm-30) REVERT: A 880 MET cc_start: 0.7293 (tpp) cc_final: 0.6634 (mpp) REVERT: A 883 ASP cc_start: 0.7974 (t70) cc_final: 0.7518 (t0) REVERT: A 907 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7673 (mtmt) REVERT: A 923 LYS cc_start: 0.7695 (mtmm) cc_final: 0.7398 (mtmm) REVERT: A 957 PHE cc_start: 0.5239 (p90) cc_final: 0.3338 (p90) outliers start: 13 outliers final: 7 residues processed: 156 average time/residue: 0.1820 time to fit residues: 39.7880 Evaluate side-chains 155 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 148 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 842 GLU 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: 0.9980 chunk 80 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 26 optimal weight: 0.0010 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 0.5980 chunk 96 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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: 0.6645 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7910 Z= 0.173 Angle : 0.511 7.407 10735 Z= 0.270 Chirality : 0.041 0.159 1273 Planarity : 0.004 0.050 1400 Dihedral : 4.180 25.961 1125 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.92 % Allowed : 15.96 % Favored : 83.11 % 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: -1.09 (0.26), residues: 1057 helix: 0.76 (0.28), residues: 367 sheet: -1.44 (0.42), residues: 147 loop : -1.58 (0.26), residues: 543 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 129 HIS 0.005 0.001 HIS A 411 PHE 0.020 0.001 PHE A 957 TYR 0.019 0.001 TYR A 879 ARG 0.002 0.000 ARG A 499 *********************** 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 157 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 150 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 153 CYS cc_start: 0.6552 (t) cc_final: 0.6265 (t) REVERT: A 282 LEU cc_start: 0.7529 (mt) cc_final: 0.7237 (mt) REVERT: A 346 ASP cc_start: 0.6470 (p0) cc_final: 0.6235 (p0) REVERT: A 355 MET cc_start: 0.4763 (tpt) cc_final: 0.4512 (tpt) REVERT: A 424 ASP cc_start: 0.7279 (p0) cc_final: 0.7026 (p0) REVERT: A 478 GLN cc_start: 0.7554 (tt0) cc_final: 0.7215 (tt0) REVERT: A 554 SER cc_start: 0.7006 (p) cc_final: 0.6737 (p) REVERT: A 663 MET cc_start: 0.8281 (ptm) cc_final: 0.8012 (ttp) REVERT: A 880 MET cc_start: 0.7170 (tpp) cc_final: 0.6526 (mpp) REVERT: A 883 ASP cc_start: 0.7958 (t70) cc_final: 0.7489 (t0) REVERT: A 907 LYS cc_start: 0.7916 (mtmt) cc_final: 0.7588 (mtmt) REVERT: A 923 LYS cc_start: 0.7629 (mtmm) cc_final: 0.7328 (mtmm) REVERT: A 957 PHE cc_start: 0.5301 (p90) cc_final: 0.3402 (p90) outliers start: 7 outliers final: 3 residues processed: 152 average time/residue: 0.1976 time to fit residues: 42.3063 Evaluate side-chains 153 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 794 VAL 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: 0.6980 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7910 Z= 0.330 Angle : 0.596 7.813 10735 Z= 0.317 Chirality : 0.044 0.171 1273 Planarity : 0.005 0.050 1400 Dihedral : 4.621 19.938 1124 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 1.98 % Allowed : 17.41 % Favored : 80.61 % 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: -1.37 (0.25), residues: 1057 helix: 0.51 (0.27), residues: 373 sheet: -1.48 (0.44), residues: 139 loop : -1.80 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 485 HIS 0.007 0.001 HIS A 411 PHE 0.024 0.002 PHE A 471 TYR 0.022 0.002 TYR A 879 ARG 0.002 0.000 ARG A 194 *********************** 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 175 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5429 (tt0) cc_final: 0.5213 (tt0) REVERT: A 239 LEU cc_start: 0.8040 (mt) cc_final: 0.7818 (mt) REVERT: A 282 LEU cc_start: 0.7562 (mt) cc_final: 0.7324 (mt) REVERT: A 328 GLU cc_start: 0.6743 (mp0) cc_final: 0.6343 (mp0) REVERT: A 346 ASP cc_start: 0.6541 (p0) cc_final: 0.6268 (p0) REVERT: A 355 MET cc_start: 0.4789 (tpt) cc_final: 0.4477 (tpt) REVERT: A 424 ASP cc_start: 0.7330 (p0) cc_final: 0.7046 (p0) REVERT: A 554 SER cc_start: 0.7049 (p) cc_final: 0.6688 (p) REVERT: A 663 MET cc_start: 0.8337 (ptm) cc_final: 0.8060 (ttp) REVERT: A 724 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8137 (tp) REVERT: A 878 ASP cc_start: 0.7236 (m-30) cc_final: 0.7003 (m-30) REVERT: A 883 ASP cc_start: 0.8027 (t70) cc_final: 0.7555 (t0) REVERT: A 907 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7687 (mtmt) REVERT: A 923 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7397 (mtmm) REVERT: A 957 PHE cc_start: 0.5589 (p90) cc_final: 0.3714 (p90) outliers start: 15 outliers final: 9 residues processed: 166 average time/residue: 0.2384 time to fit residues: 54.7620 Evaluate side-chains 165 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 155 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 842 GLU 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: 0.0000 chunk 58 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.1942 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= 0.197 Angle : 0.546 13.403 10735 Z= 0.282 Chirality : 0.042 0.160 1273 Planarity : 0.004 0.068 1400 Dihedral : 4.294 18.575 1124 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 1.98 % Allowed : 20.05 % Favored : 77.97 % 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: -1.19 (0.26), residues: 1057 helix: 0.78 (0.28), residues: 367 sheet: -1.44 (0.43), residues: 145 loop : -1.75 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 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 0.001 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 169 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 153 CYS cc_start: 0.6550 (t) cc_final: 0.6313 (t) REVERT: A 223 THR cc_start: 0.7970 (OUTLIER) cc_final: 0.7754 (m) REVERT: A 239 LEU cc_start: 0.8010 (mt) cc_final: 0.7763 (mt) REVERT: A 282 LEU cc_start: 0.7553 (mt) cc_final: 0.7337 (mt) REVERT: A 328 GLU cc_start: 0.6705 (mp0) cc_final: 0.6322 (mp0) REVERT: A 346 ASP cc_start: 0.6478 (p0) cc_final: 0.6232 (p0) REVERT: A 355 MET cc_start: 0.4727 (tpt) cc_final: 0.4432 (tpt) REVERT: A 424 ASP cc_start: 0.7250 (p0) cc_final: 0.6975 (p0) REVERT: A 478 GLN cc_start: 0.7575 (tt0) cc_final: 0.7177 (tt0) REVERT: A 554 SER cc_start: 0.7054 (p) cc_final: 0.6810 (p) REVERT: A 663 MET cc_start: 0.8300 (ptm) cc_final: 0.8067 (ttp) REVERT: A 880 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6304 (mpp) REVERT: A 883 ASP cc_start: 0.7997 (t70) cc_final: 0.7495 (t0) REVERT: A 923 LYS cc_start: 0.7668 (mtmm) cc_final: 0.7363 (mtmm) REVERT: A 935 LYS cc_start: 0.8227 (mmmm) cc_final: 0.8018 (mmmm) REVERT: A 957 PHE cc_start: 0.5599 (p90) cc_final: 0.3722 (p90) outliers start: 15 outliers final: 8 residues processed: 163 average time/residue: 0.1950 time to fit residues: 43.9139 Evaluate side-chains 157 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU 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 316 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 719 SER Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 880 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 2.9990 chunk 93 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 54 optimal weight: 0.0570 chunk 99 optimal weight: 20.0000 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7910 Z= 0.177 Angle : 0.530 9.837 10735 Z= 0.274 Chirality : 0.041 0.159 1273 Planarity : 0.004 0.049 1400 Dihedral : 4.128 18.535 1124 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 2.24 % Allowed : 20.18 % Favored : 77.57 % 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: -1.09 (0.26), residues: 1057 helix: 0.90 (0.28), residues: 369 sheet: -1.45 (0.42), residues: 147 loop : -1.69 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.021 0.001 PHE A 957 TYR 0.020 0.001 TYR A 879 ARG 0.003 0.000 ARG A 605 *********************** 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 167 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7689 (m) REVERT: A 239 LEU cc_start: 0.8014 (mt) cc_final: 0.7748 (mt) REVERT: A 282 LEU cc_start: 0.7552 (mt) cc_final: 0.7303 (mt) REVERT: A 328 GLU cc_start: 0.6704 (mp0) cc_final: 0.6285 (mp0) REVERT: A 355 MET cc_start: 0.4705 (tpt) cc_final: 0.4435 (tpt) REVERT: A 424 ASP cc_start: 0.7264 (p0) cc_final: 0.6998 (p0) REVERT: A 478 GLN cc_start: 0.7573 (tt0) cc_final: 0.7074 (tt0) REVERT: A 554 SER cc_start: 0.7192 (p) cc_final: 0.6917 (p) REVERT: A 663 MET cc_start: 0.8274 (ptm) cc_final: 0.8032 (ttp) REVERT: A 730 ILE cc_start: 0.8212 (mt) cc_final: 0.7783 (mm) REVERT: A 883 ASP cc_start: 0.8003 (t70) cc_final: 0.7492 (t0) REVERT: A 907 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7607 (mtmt) REVERT: A 923 LYS cc_start: 0.7629 (mtmm) cc_final: 0.7325 (mtmm) REVERT: A 935 LYS cc_start: 0.8176 (mmmm) cc_final: 0.7955 (mmmm) REVERT: A 957 PHE cc_start: 0.5577 (p90) cc_final: 0.3620 (p90) outliers start: 17 outliers final: 9 residues processed: 159 average time/residue: 0.1927 time to fit residues: 42.3454 Evaluate side-chains 158 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 148 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 182 LEU 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 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 794 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 75 optimal weight: 0.0270 chunk 87 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 103 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 713 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6661 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7910 Z= 0.181 Angle : 0.534 8.740 10735 Z= 0.277 Chirality : 0.041 0.157 1273 Planarity : 0.004 0.064 1400 Dihedral : 4.076 17.870 1124 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.76 % Favored : 92.05 % Rotamer: Outliers : 2.37 % Allowed : 20.58 % Favored : 77.04 % 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: 0.99 (0.28), residues: 369 sheet: -1.38 (0.42), residues: 147 loop : -1.68 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.020 0.001 PHE A 957 TYR 0.021 0.001 TYR A 879 ARG 0.003 0.000 ARG A 605 *********************** 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 172 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7864 (mtmt) cc_final: 0.7653 (mtmt) REVERT: A 223 THR cc_start: 0.7934 (OUTLIER) cc_final: 0.7684 (m) REVERT: A 239 LEU cc_start: 0.8012 (mt) cc_final: 0.7747 (mt) REVERT: A 282 LEU cc_start: 0.7536 (mt) cc_final: 0.7316 (mt) REVERT: A 355 MET cc_start: 0.4733 (tpt) cc_final: 0.4432 (tpt) REVERT: A 424 ASP cc_start: 0.7263 (p0) cc_final: 0.6989 (p0) REVERT: A 554 SER cc_start: 0.7217 (p) cc_final: 0.6913 (p) REVERT: A 663 MET cc_start: 0.8278 (ptm) cc_final: 0.8031 (ttp) REVERT: A 724 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7997 (tp) REVERT: A 762 GLN cc_start: 0.8357 (mp10) cc_final: 0.7971 (mp10) REVERT: A 869 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6321 (mt) REVERT: A 883 ASP cc_start: 0.8008 (t70) cc_final: 0.7511 (t0) REVERT: A 907 LYS cc_start: 0.7965 (mtmt) cc_final: 0.7589 (mtmt) REVERT: A 923 LYS cc_start: 0.7635 (mtmm) cc_final: 0.7334 (mtmm) REVERT: A 935 LYS cc_start: 0.8163 (mmmm) cc_final: 0.7945 (mmmm) REVERT: A 957 PHE cc_start: 0.5576 (p90) cc_final: 0.3602 (p90) outliers start: 18 outliers final: 12 residues processed: 164 average time/residue: 0.1841 time to fit residues: 42.1103 Evaluate side-chains 168 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 182 LEU 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 316 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 483 SER 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 724 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 869 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN A 824 ASN A 835 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7910 Z= 0.334 Angle : 0.616 9.291 10735 Z= 0.325 Chirality : 0.045 0.170 1273 Planarity : 0.005 0.064 1400 Dihedral : 4.610 20.118 1124 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 2.51 % Allowed : 21.11 % 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: -1.32 (0.26), residues: 1057 helix: 0.62 (0.28), residues: 373 sheet: -1.44 (0.42), residues: 145 loop : -1.83 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 485 HIS 0.011 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 605 *********************** 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 173 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7949 (mtmt) cc_final: 0.7737 (mtmt) REVERT: A 223 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7789 (m) REVERT: A 239 LEU cc_start: 0.8025 (mt) cc_final: 0.7779 (mt) REVERT: A 282 LEU cc_start: 0.7566 (mt) cc_final: 0.7341 (mt) REVERT: A 355 MET cc_start: 0.4745 (tpt) cc_final: 0.4462 (tpt) REVERT: A 424 ASP cc_start: 0.7286 (p0) cc_final: 0.7000 (p0) REVERT: A 554 SER cc_start: 0.7228 (p) cc_final: 0.6893 (p) REVERT: A 664 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7990 (mt) REVERT: A 724 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8077 (tp) REVERT: A 762 GLN cc_start: 0.8414 (mp10) cc_final: 0.7916 (mp10) REVERT: A 869 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6458 (mt) REVERT: A 883 ASP cc_start: 0.8058 (t70) cc_final: 0.7554 (t0) REVERT: A 897 ASP cc_start: 0.7803 (m-30) cc_final: 0.7313 (m-30) REVERT: A 923 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7421 (mtmm) outliers start: 19 outliers final: 12 residues processed: 165 average time/residue: 0.1874 time to fit residues: 43.1361 Evaluate side-chains 165 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 182 LEU 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 316 MET Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 493 VAL 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 794 VAL Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 924 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.3980 chunk 96 optimal weight: 0.9980 chunk 98 optimal weight: 0.0570 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 75 optimal weight: 0.0570 chunk 29 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- 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: 0.6666 moved from start: 0.2336 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= 0.174 Angle : 0.543 12.925 10735 Z= 0.282 Chirality : 0.041 0.158 1273 Planarity : 0.004 0.056 1400 Dihedral : 4.203 18.570 1124 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.10 % Favored : 92.81 % Rotamer: Outliers : 2.37 % Allowed : 21.64 % Favored : 75.99 % 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: -1.03 (0.26), residues: 1057 helix: 0.94 (0.28), residues: 369 sheet: -1.30 (0.43), residues: 142 loop : -1.71 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.024 0.002 PHE A 957 TYR 0.024 0.001 TYR A 879 ARG 0.003 0.000 ARG A 605 *********************** 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 164 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.7938 (OUTLIER) cc_final: 0.7672 (m) REVERT: A 225 PHE cc_start: 0.8098 (p90) cc_final: 0.7869 (p90) REVERT: A 239 LEU cc_start: 0.8017 (mt) cc_final: 0.7750 (mt) REVERT: A 282 LEU cc_start: 0.7544 (mt) cc_final: 0.7316 (mt) REVERT: A 355 MET cc_start: 0.4714 (tpt) cc_final: 0.4434 (tpt) REVERT: A 424 ASP cc_start: 0.7219 (p0) cc_final: 0.6933 (p0) REVERT: A 554 SER cc_start: 0.7215 (p) cc_final: 0.6886 (p) REVERT: A 688 LYS cc_start: 0.7450 (mptt) cc_final: 0.6818 (mptt) REVERT: A 724 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7957 (tp) REVERT: A 869 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6301 (mt) REVERT: A 883 ASP cc_start: 0.8026 (t70) cc_final: 0.7491 (t0) REVERT: A 923 LYS cc_start: 0.7627 (mtmm) cc_final: 0.7324 (mtmm) REVERT: A 957 PHE cc_start: 0.5582 (p90) cc_final: 0.3589 (p90) outliers start: 18 outliers final: 12 residues processed: 157 average time/residue: 0.1854 time to fit residues: 40.5909 Evaluate side-chains 161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 218 MET 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 271 THR Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain A residue 414 ASP 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 724 LEU Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 869 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 98 optimal weight: 0.0270 chunk 84 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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: 0.6660 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7910 Z= 0.185 Angle : 0.551 13.207 10735 Z= 0.286 Chirality : 0.041 0.158 1273 Planarity : 0.004 0.052 1400 Dihedral : 4.115 18.429 1124 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.85 % Favored : 92.05 % Rotamer: Outliers : 1.85 % Allowed : 21.90 % Favored : 76.25 % 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: 0.99 (0.28), residues: 369 sheet: -1.38 (0.42), residues: 147 loop : -1.69 (0.26), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 PHE 0.022 0.002 PHE A 487 TYR 0.027 0.002 TYR A 345 ARG 0.002 0.000 ARG A 766 ********************** 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 159 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.7936 (OUTLIER) cc_final: 0.7650 (m) REVERT: A 235 THR cc_start: 0.7798 (t) cc_final: 0.7448 (m) REVERT: A 239 LEU cc_start: 0.8013 (mt) cc_final: 0.7734 (mt) REVERT: A 282 LEU cc_start: 0.7545 (mt) cc_final: 0.7333 (mt) REVERT: A 355 MET cc_start: 0.4704 (tpt) cc_final: 0.4444 (tpt) REVERT: A 424 ASP cc_start: 0.7247 (p0) cc_final: 0.6969 (p0) REVERT: A 478 GLN cc_start: 0.7547 (tt0) cc_final: 0.7105 (tt0) REVERT: A 554 SER cc_start: 0.7228 (p) cc_final: 0.6887 (p) REVERT: A 688 LYS cc_start: 0.7464 (mptt) cc_final: 0.6840 (mptt) REVERT: A 869 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6302 (mt) REVERT: A 883 ASP cc_start: 0.8034 (t70) cc_final: 0.7515 (t0) REVERT: A 957 PHE cc_start: 0.5565 (p90) cc_final: 0.3574 (p90) outliers start: 14 outliers final: 10 residues processed: 154 average time/residue: 0.2117 time to fit residues: 46.0826 Evaluate side-chains 155 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 143 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 182 LEU 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 316 MET Chi-restraints excluded: chain A residue 414 ASP 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 794 VAL Chi-restraints excluded: chain A residue 869 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.174858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.148502 restraints weight = 10834.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152493 restraints weight = 6035.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155164 restraints weight = 4034.263| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7910 Z= 0.271 Angle : 0.591 12.862 10735 Z= 0.310 Chirality : 0.043 0.160 1273 Planarity : 0.004 0.057 1400 Dihedral : 4.396 19.199 1124 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.39 % Rotamer: Outliers : 2.11 % Allowed : 21.37 % Favored : 76.52 % 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: -1.20 (0.26), residues: 1057 helix: 0.76 (0.28), residues: 373 sheet: -1.39 (0.42), residues: 145 loop : -1.79 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 485 HIS 0.010 0.001 HIS A 411 PHE 0.023 0.002 PHE A 471 TYR 0.033 0.002 TYR A 345 ARG 0.002 0.000 ARG A 605 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2975.08 seconds wall clock time: 54 minutes 32.21 seconds (3272.21 seconds total)