Starting phenix.real_space_refine on Wed Feb 12 10:43:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqs_24635/02_2025/7rqs_24635.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqs_24635/02_2025/7rqs_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_24635/02_2025/7rqs_24635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqs_24635/02_2025/7rqs_24635.map" model { file = "/net/cci-nas-00/data/ceres_data/7rqs_24635/02_2025/7rqs_24635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqs_24635/02_2025/7rqs_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.56, per 1000 atoms: 0.84 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: 2.19 Conformation dependent library (CDL) restraints added in 984.9 milliseconds 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: 1.02 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: 3.06 Time building geometry restraints manager: 2.48 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: 7.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 23.760 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- 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 : 0.710 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: 0.2258 time to fit residues: 48.3767 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 : 0.790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.175239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.148723 restraints weight = 10726.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152712 restraints weight = 6001.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155486 restraints weight = 4035.679| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6690 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 : 0.809 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7541 (mtmt) REVERT: A 153 CYS cc_start: 0.6645 (t) cc_final: 0.6329 (t) REVERT: A 239 LEU cc_start: 0.8096 (mt) cc_final: 0.7863 (mt) REVERT: A 282 LEU cc_start: 0.7549 (mt) cc_final: 0.7247 (mt) REVERT: A 346 ASP cc_start: 0.6601 (p0) cc_final: 0.6345 (p0) REVERT: A 355 MET cc_start: 0.4932 (tpt) cc_final: 0.4626 (tpt) REVERT: A 424 ASP cc_start: 0.7327 (p0) cc_final: 0.7041 (p0) REVERT: A 662 ASN cc_start: 0.7514 (m-40) cc_final: 0.7287 (m-40) REVERT: A 688 LYS cc_start: 0.7488 (mptt) cc_final: 0.6795 (mptt) REVERT: A 870 GLU cc_start: 0.6834 (tm-30) cc_final: 0.6625 (tm-30) REVERT: A 880 MET cc_start: 0.7304 (tpp) cc_final: 0.6614 (mpp) REVERT: A 883 ASP cc_start: 0.8003 (t70) cc_final: 0.7569 (t0) REVERT: A 907 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7697 (mtmt) REVERT: A 923 LYS cc_start: 0.7728 (mtmm) cc_final: 0.7409 (mtmm) REVERT: A 957 PHE cc_start: 0.5206 (p90) cc_final: 0.3291 (p90) outliers start: 13 outliers final: 7 residues processed: 156 average time/residue: 0.1833 time to fit residues: 39.6671 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 95 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.172602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146258 restraints weight = 10896.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150211 restraints weight = 6067.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152814 restraints weight = 4058.065| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 7910 Z= 0.423 Angle : 0.649 8.901 10735 Z= 0.349 Chirality : 0.046 0.174 1273 Planarity : 0.005 0.051 1400 Dihedral : 5.007 24.483 1125 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 1.98 % Allowed : 14.91 % 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: -1.61 (0.25), residues: 1057 helix: 0.17 (0.27), residues: 373 sheet: -1.44 (0.44), residues: 136 loop : -1.89 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 485 HIS 0.006 0.001 HIS A 411 PHE 0.025 0.002 PHE A 471 TYR 0.024 0.002 TYR A 879 ARG 0.003 0.000 ARG A 898 *********************** 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 174 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 0.966 Fit side-chains revert: symmetry clash REVERT: A 282 LEU cc_start: 0.7582 (mt) cc_final: 0.7324 (mt) REVERT: A 328 GLU cc_start: 0.6747 (mp0) cc_final: 0.6383 (mp0) REVERT: A 346 ASP cc_start: 0.6634 (p0) cc_final: 0.6323 (p0) REVERT: A 355 MET cc_start: 0.4986 (tpt) cc_final: 0.4605 (tpt) REVERT: A 424 ASP cc_start: 0.7267 (p0) cc_final: 0.6995 (p0) REVERT: A 496 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: A 604 LEU cc_start: 0.7550 (tt) cc_final: 0.7313 (tt) REVERT: A 663 MET cc_start: 0.8409 (ptm) cc_final: 0.8122 (ttp) REVERT: A 878 ASP cc_start: 0.7334 (m-30) cc_final: 0.6999 (m-30) REVERT: A 883 ASP cc_start: 0.8053 (t70) cc_final: 0.7604 (t0) REVERT: A 897 ASP cc_start: 0.7799 (m-30) cc_final: 0.7337 (m-30) REVERT: A 907 LYS cc_start: 0.8087 (mtmt) cc_final: 0.7732 (mtmt) REVERT: A 923 LYS cc_start: 0.7786 (mtmm) cc_final: 0.7441 (mtmm) REVERT: A 957 PHE cc_start: 0.5634 (p90) cc_final: 0.3713 (p90) outliers start: 15 outliers final: 9 residues processed: 162 average time/residue: 0.2034 time to fit residues: 45.5639 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 : 0.833 ------------------------------------------------------------------------------- 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 218 MET Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 773 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 0.0670 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 85 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.175304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.148996 restraints weight = 10831.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.153034 restraints weight = 6012.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155718 restraints weight = 4007.289| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.1914 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= 0.197 Angle : 0.530 7.440 10735 Z= 0.281 Chirality : 0.042 0.163 1273 Planarity : 0.004 0.057 1400 Dihedral : 4.371 19.195 1124 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.76 % Favored : 92.15 % Rotamer: Outliers : 1.72 % Allowed : 18.60 % Favored : 79.68 % 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: 0.62 (0.28), residues: 367 sheet: -1.46 (0.43), residues: 145 loop : -1.77 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 129 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 0.002 0.000 ARG A 766 *********************** 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 156 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.825 Fit side-chains REVERT: A 282 LEU cc_start: 0.7569 (mt) cc_final: 0.7342 (mt) REVERT: A 328 GLU cc_start: 0.6745 (mp0) cc_final: 0.6354 (mp0) REVERT: A 346 ASP cc_start: 0.6523 (p0) cc_final: 0.6206 (p0) REVERT: A 355 MET cc_start: 0.4920 (tpt) cc_final: 0.4538 (tpt) REVERT: A 424 ASP cc_start: 0.7211 (p0) cc_final: 0.6893 (p0) REVERT: A 478 GLN cc_start: 0.7600 (tt0) cc_final: 0.7010 (tt0) REVERT: A 496 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6651 (mm-30) REVERT: A 724 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8093 (tp) REVERT: A 869 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.6284 (mt) REVERT: A 880 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6261 (mpp) REVERT: A 883 ASP cc_start: 0.8025 (t70) cc_final: 0.7530 (t0) REVERT: A 923 LYS cc_start: 0.7707 (mtmm) cc_final: 0.7373 (mtmm) REVERT: A 935 LYS cc_start: 0.8242 (mmmm) cc_final: 0.8005 (mmmm) REVERT: A 957 PHE cc_start: 0.5583 (p90) cc_final: 0.3632 (p90) outliers start: 13 outliers final: 3 residues processed: 150 average time/residue: 0.1928 time to fit residues: 40.2743 Evaluate side-chains 153 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 496 GLU Chi-restraints excluded: chain A residue 724 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 81 optimal weight: 0.0010 chunk 100 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 0.0570 overall best weight: 0.3904 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.176529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.150246 restraints weight = 10784.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.154225 restraints weight = 6004.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156823 restraints weight = 4037.265| |-----------------------------------------------------------------------------| r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7910 Z= 0.157 Angle : 0.522 12.203 10735 Z= 0.270 Chirality : 0.041 0.161 1273 Planarity : 0.004 0.048 1400 Dihedral : 4.122 18.082 1124 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.47 % Favored : 92.43 % Rotamer: Outliers : 2.37 % Allowed : 19.92 % Favored : 77.70 % 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: -1.10 (0.26), residues: 1057 helix: 0.82 (0.28), residues: 369 sheet: -1.36 (0.43), residues: 142 loop : -1.69 (0.25), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 623 HIS 0.008 0.001 HIS A 411 PHE 0.021 0.001 PHE A 957 TYR 0.018 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 175 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 223 THR cc_start: 0.7953 (OUTLIER) cc_final: 0.7722 (m) REVERT: A 282 LEU cc_start: 0.7541 (mt) cc_final: 0.7313 (mt) REVERT: A 328 GLU cc_start: 0.6752 (mp0) cc_final: 0.6351 (mp0) REVERT: A 355 MET cc_start: 0.4907 (tpt) cc_final: 0.4536 (tpt) REVERT: A 424 ASP cc_start: 0.7213 (p0) cc_final: 0.6951 (p0) REVERT: A 724 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7978 (tp) REVERT: A 762 GLN cc_start: 0.8267 (mp10) cc_final: 0.7705 (mp10) REVERT: A 880 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6171 (mpp) REVERT: A 883 ASP cc_start: 0.8024 (t70) cc_final: 0.7556 (t0) REVERT: A 897 ASP cc_start: 0.7804 (m-30) cc_final: 0.7297 (m-30) REVERT: A 907 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7568 (mtmt) REVERT: A 923 LYS cc_start: 0.7660 (mtmm) cc_final: 0.7336 (mtmm) REVERT: A 935 LYS cc_start: 0.8209 (mmmm) cc_final: 0.7974 (mmmm) REVERT: A 957 PHE cc_start: 0.5545 (p90) cc_final: 0.3455 (p90) outliers start: 18 outliers final: 10 residues processed: 166 average time/residue: 0.1936 time to fit residues: 44.5853 Evaluate side-chains 168 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 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 959 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 17 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 824 ASN A 835 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.175079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148674 restraints weight = 10829.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.152635 restraints weight = 6029.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.155300 restraints weight = 4050.397| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7910 Z= 0.232 Angle : 0.558 10.577 10735 Z= 0.291 Chirality : 0.042 0.163 1273 Planarity : 0.004 0.062 1400 Dihedral : 4.284 19.177 1124 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 2.77 % Allowed : 20.18 % 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: -1.15 (0.26), residues: 1057 helix: 0.80 (0.28), residues: 367 sheet: -1.34 (0.43), residues: 145 loop : -1.75 (0.25), residues: 545 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 0.021 0.002 PHE A 471 TYR 0.020 0.001 TYR A 879 ARG 0.001 0.000 ARG A 499 *********************** 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 173 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 152 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7765 (m) REVERT: A 282 LEU cc_start: 0.7582 (mt) cc_final: 0.7359 (mt) REVERT: A 328 GLU cc_start: 0.6781 (mp0) cc_final: 0.6358 (mp0) REVERT: A 355 MET cc_start: 0.4901 (tpt) cc_final: 0.4589 (tpt) REVERT: A 424 ASP cc_start: 0.7263 (p0) cc_final: 0.6995 (p0) REVERT: A 724 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8024 (tp) REVERT: A 762 GLN cc_start: 0.8287 (mp10) cc_final: 0.7693 (mp10) REVERT: A 869 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6260 (mt) REVERT: A 880 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6290 (mpp) REVERT: A 883 ASP cc_start: 0.8058 (t70) cc_final: 0.7589 (t0) REVERT: A 897 ASP cc_start: 0.7855 (m-30) cc_final: 0.7359 (m-30) REVERT: A 923 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7393 (mtmm) REVERT: A 957 PHE cc_start: 0.5561 (p90) cc_final: 0.3566 (p90) outliers start: 21 outliers final: 14 residues processed: 163 average time/residue: 0.1952 time to fit residues: 43.9247 Evaluate side-chains 166 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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 570 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain A residue 773 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 47 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 30.0000 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.175845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149358 restraints weight = 10891.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153437 restraints weight = 6066.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.156067 restraints weight = 4051.607| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2211 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= 0.211 Angle : 0.559 13.021 10735 Z= 0.287 Chirality : 0.042 0.163 1273 Planarity : 0.004 0.051 1400 Dihedral : 4.239 18.857 1124 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.33 % Favored : 91.58 % Rotamer: Outliers : 2.64 % Allowed : 21.24 % 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: -1.12 (0.26), residues: 1057 helix: 0.86 (0.28), residues: 366 sheet: -1.30 (0.43), residues: 145 loop : -1.75 (0.25), residues: 546 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 0.019 0.001 PHE A 957 TYR 0.023 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 to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.7996 (OUTLIER) cc_final: 0.7765 (m) REVERT: A 282 LEU cc_start: 0.7571 (mt) cc_final: 0.7345 (mt) REVERT: A 328 GLU cc_start: 0.6783 (mp0) cc_final: 0.6361 (mp0) REVERT: A 355 MET cc_start: 0.4906 (tpt) cc_final: 0.4590 (tpt) REVERT: A 424 ASP cc_start: 0.7248 (p0) cc_final: 0.6977 (p0) REVERT: A 478 GLN cc_start: 0.7585 (tt0) cc_final: 0.7116 (tt0) REVERT: A 724 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8002 (tp) REVERT: A 869 LEU cc_start: 0.6568 (OUTLIER) cc_final: 0.6280 (mt) REVERT: A 880 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6281 (mpp) REVERT: A 883 ASP cc_start: 0.8064 (t70) cc_final: 0.7576 (t0) REVERT: A 923 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7375 (mtmm) REVERT: A 957 PHE cc_start: 0.5549 (p90) cc_final: 0.3605 (p90) outliers start: 20 outliers final: 12 residues processed: 162 average time/residue: 0.1843 time to fit residues: 41.2842 Evaluate side-chains 163 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 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 880 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 102 optimal weight: 0.0870 chunk 39 optimal weight: 0.0040 chunk 58 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.8174 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.175312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.148872 restraints weight = 10859.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152879 restraints weight = 6046.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155552 restraints weight = 4066.750| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7910 Z= 0.229 Angle : 0.563 9.613 10735 Z= 0.293 Chirality : 0.042 0.163 1273 Planarity : 0.004 0.067 1400 Dihedral : 4.294 19.286 1124 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.23 % Favored : 91.58 % Rotamer: Outliers : 2.77 % Allowed : 21.64 % Favored : 75.59 % 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: 0.84 (0.28), residues: 366 sheet: -1.27 (0.43), residues: 145 loop : -1.75 (0.26), residues: 546 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 0.021 0.001 PHE A 471 TYR 0.025 0.002 TYR A 879 ARG 0.001 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 169 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.8011 (OUTLIER) cc_final: 0.7776 (m) REVERT: A 282 LEU cc_start: 0.7582 (mt) cc_final: 0.7352 (mt) REVERT: A 328 GLU cc_start: 0.6780 (mp0) cc_final: 0.6358 (mp0) REVERT: A 355 MET cc_start: 0.4892 (tpt) cc_final: 0.4582 (tpt) REVERT: A 424 ASP cc_start: 0.7256 (p0) cc_final: 0.6983 (p0) REVERT: A 478 GLN cc_start: 0.7573 (tt0) cc_final: 0.7106 (tt0) REVERT: A 702 LEU cc_start: 0.7826 (tt) cc_final: 0.7551 (tp) REVERT: A 724 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8016 (tp) REVERT: A 762 GLN cc_start: 0.8399 (mp10) cc_final: 0.7850 (mp10) REVERT: A 869 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6286 (mt) REVERT: A 880 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6320 (mpp) REVERT: A 883 ASP cc_start: 0.8083 (t70) cc_final: 0.7586 (t0) REVERT: A 923 LYS cc_start: 0.7713 (mtmm) cc_final: 0.7391 (mtmm) REVERT: A 957 PHE cc_start: 0.5566 (p90) cc_final: 0.3645 (p90) outliers start: 21 outliers final: 16 residues processed: 159 average time/residue: 0.2065 time to fit residues: 45.9004 Evaluate side-chains 167 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 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 472 LEU 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 740 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 10.0000 chunk 57 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.175432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148876 restraints weight = 11072.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.152929 restraints weight = 6133.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155593 restraints weight = 4092.936| |-----------------------------------------------------------------------------| r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7910 Z= 0.227 Angle : 0.574 11.611 10735 Z= 0.296 Chirality : 0.042 0.174 1273 Planarity : 0.004 0.055 1400 Dihedral : 4.295 18.862 1124 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.51 % Favored : 91.30 % Rotamer: Outliers : 2.77 % Allowed : 21.50 % Favored : 75.73 % 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: 0.78 (0.28), residues: 372 sheet: -1.28 (0.43), residues: 145 loop : -1.75 (0.26), residues: 540 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 0.002 PHE A 471 TYR 0.026 0.002 TYR A 879 ARG 0.001 0.000 ARG A 194 *********************** 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 171 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7767 (m) REVERT: A 282 LEU cc_start: 0.7579 (mt) cc_final: 0.7350 (mt) REVERT: A 328 GLU cc_start: 0.6786 (mp0) cc_final: 0.6354 (mp0) REVERT: A 355 MET cc_start: 0.4855 (tpt) cc_final: 0.4542 (tpt) REVERT: A 424 ASP cc_start: 0.7245 (p0) cc_final: 0.6978 (p0) REVERT: A 724 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8018 (tp) REVERT: A 762 GLN cc_start: 0.8394 (mp10) cc_final: 0.7784 (mp10) REVERT: A 869 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6272 (mt) REVERT: A 880 MET cc_start: 0.7081 (OUTLIER) cc_final: 0.6275 (mpp) REVERT: A 883 ASP cc_start: 0.8085 (t70) cc_final: 0.7579 (t0) REVERT: A 897 ASP cc_start: 0.7822 (m-30) cc_final: 0.7357 (m-30) REVERT: A 923 LYS cc_start: 0.7712 (mtmm) cc_final: 0.7374 (mtmm) REVERT: A 957 PHE cc_start: 0.5561 (p90) cc_final: 0.3599 (p90) outliers start: 21 outliers final: 15 residues processed: 160 average time/residue: 0.1896 time to fit residues: 41.8835 Evaluate side-chains 167 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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 271 THR 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 570 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 740 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 52 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.175118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.148661 restraints weight = 10949.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.152662 restraints weight = 6143.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155361 restraints weight = 4115.222| |-----------------------------------------------------------------------------| r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7910 Z= 0.257 Angle : 0.607 13.501 10735 Z= 0.312 Chirality : 0.043 0.169 1273 Planarity : 0.004 0.057 1400 Dihedral : 4.402 19.451 1124 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.39 % Rotamer: Outliers : 2.64 % Allowed : 21.64 % Favored : 75.73 % 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: -1.16 (0.26), residues: 1057 helix: 0.71 (0.28), residues: 374 sheet: -1.30 (0.43), residues: 145 loop : -1.73 (0.26), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 485 HIS 0.010 0.001 HIS A 411 PHE 0.022 0.002 PHE A 471 TYR 0.028 0.002 TYR A 879 ARG 0.002 0.000 ARG A 194 ********************** 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 165 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 223 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7786 (m) REVERT: A 282 LEU cc_start: 0.7588 (mt) cc_final: 0.7361 (mt) REVERT: A 328 GLU cc_start: 0.6786 (mp0) cc_final: 0.6358 (mp0) REVERT: A 355 MET cc_start: 0.4863 (tpt) cc_final: 0.4546 (tpt) REVERT: A 424 ASP cc_start: 0.7256 (p0) cc_final: 0.6982 (p0) REVERT: A 724 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8043 (tp) REVERT: A 762 GLN cc_start: 0.8415 (mp10) cc_final: 0.7851 (mp10) REVERT: A 869 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6256 (mt) REVERT: A 880 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6287 (mpp) REVERT: A 883 ASP cc_start: 0.8084 (t70) cc_final: 0.7588 (t0) REVERT: A 897 ASP cc_start: 0.7833 (m-30) cc_final: 0.7354 (m-30) REVERT: A 923 LYS cc_start: 0.7724 (mtmm) cc_final: 0.7411 (mtmm) REVERT: A 957 PHE cc_start: 0.5540 (p90) cc_final: 0.3590 (p90) outliers start: 20 outliers final: 16 residues processed: 155 average time/residue: 0.1850 time to fit residues: 40.2649 Evaluate side-chains 165 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 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 271 THR 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 570 GLN Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 740 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 88 optimal weight: 0.4980 chunk 104 optimal weight: 0.4980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.177291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.150970 restraints weight = 10906.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.155077 restraints weight = 6103.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.157832 restraints weight = 4073.559| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.2503 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= 0.186 Angle : 0.568 12.322 10735 Z= 0.289 Chirality : 0.042 0.165 1273 Planarity : 0.004 0.051 1400 Dihedral : 4.156 18.770 1124 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.76 % Favored : 92.05 % Rotamer: Outliers : 2.24 % Allowed : 21.90 % Favored : 75.86 % 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: -0.98 (0.26), residues: 1057 helix: 0.95 (0.28), residues: 370 sheet: -1.25 (0.43), residues: 147 loop : -1.66 (0.26), residues: 540 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 0.021 0.001 PHE A 957 TYR 0.025 0.001 TYR A 879 ARG 0.001 0.000 ARG A 766 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3931.37 seconds wall clock time: 70 minutes 59.25 seconds (4259.25 seconds total)