Starting phenix.real_space_refine on Tue Feb 3 23:05:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rqs_24635/02_2026/7rqs_24635.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rqs_24635/02_2026/7rqs_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_2026/7rqs_24635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rqs_24635/02_2026/7rqs_24635.map" model { file = "/net/cci-nas-00/data/ceres_data/7rqs_24635/02_2026/7rqs_24635.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rqs_24635/02_2026/7rqs_24635.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: {'GLU:plan': 21, 'ARG:plan': 19, 'TYR:plan': 20, 'PHE:plan': 15, 'TRP:plan': 5, 'GLN:plan1': 5, 'ASP:plan': 7, 'HIS:plan': 3, 'ASN:plan1': 4} 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: 1.36, per 1000 atoms: 0.17 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: 0.48 Conformation dependent library (CDL) restraints added in 220.8 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: 0.31 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: 1.51 Time building geometry restraints manager: 0.63 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: 8.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.260 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.200 ------------------------------------------------------------------------------- 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= 0.131 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.007 0.000 ARG A 766 TYR 0.023 0.001 TYR A 799 PHE 0.010 0.001 PHE A 471 TRP 0.007 0.001 TRP A 129 HIS 0.002 0.001 HIS A 710 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7910) covalent geometry : angle 0.54388 (10735) hydrogen bonds : bond 0.21747 ( 318) hydrogen bonds : angle 7.56207 ( 924) *********************** 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 : 0.167 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: 0.7122 (mp) cc_final: 0.6820 (mp) REVERT: A 282 LEU cc_start: 0.7431 (mt) cc_final: 0.7166 (mt) REVERT: A 328 GLU cc_start: 0.6634 (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: 0.0773 time to fit residues: 16.5464 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 : 0.240 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 = 0.4099 r_free = 0.4099 target = 0.174389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147653 restraints weight = 10794.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.151690 restraints weight = 6036.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154408 restraints weight = 4037.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.156210 restraints weight = 3048.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157064 restraints weight = 2508.917| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7910 Z= 0.237 Angle : 0.627 8.626 10735 Z= 0.335 Chirality : 0.045 0.188 1273 Planarity : 0.005 0.061 1400 Dihedral : 4.754 32.042 1125 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 1.72 % Allowed : 10.29 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.25), residues: 1057 helix: 0.39 (0.27), residues: 371 sheet: -1.37 (0.43), residues: 144 loop : -1.75 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 499 TYR 0.015 0.002 TYR A 385 PHE 0.023 0.002 PHE A 471 TRP 0.018 0.002 TRP A 485 HIS 0.008 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 7910) covalent geometry : angle 0.62731 (10735) hydrogen bonds : bond 0.04608 ( 318) hydrogen bonds : angle 5.91108 ( 924) *********************** 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 166 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 0.194 Fit side-chains revert: symmetry clash REVERT: A 153 CYS cc_start: 0.6600 (t) cc_final: 0.6292 (t) REVERT: A 239 LEU cc_start: 0.8099 (mt) cc_final: 0.7859 (mt) REVERT: A 280 PRO cc_start: 0.7072 (Cg_endo) cc_final: 0.6862 (Cg_exo) REVERT: A 282 LEU cc_start: 0.7573 (mt) cc_final: 0.7283 (mt) REVERT: A 346 ASP cc_start: 0.6580 (p0) cc_final: 0.6330 (p0) REVERT: A 355 MET cc_start: 0.4827 (tpt) cc_final: 0.4538 (tpt) REVERT: A 424 ASP cc_start: 0.7319 (p0) cc_final: 0.7023 (p0) REVERT: A 482 ASN cc_start: 0.7710 (m-40) cc_final: 0.7091 (m110) REVERT: A 487 PHE cc_start: 0.7788 (t80) cc_final: 0.7576 (t80) REVERT: A 557 ILE cc_start: 0.7464 (mm) cc_final: 0.7256 (mm) REVERT: A 662 ASN cc_start: 0.7504 (m-40) cc_final: 0.7287 (m-40) REVERT: A 883 ASP cc_start: 0.8010 (t70) cc_final: 0.7567 (t0) REVERT: A 923 LYS cc_start: 0.7738 (mtmm) cc_final: 0.7424 (mtmm) REVERT: A 957 PHE cc_start: 0.5318 (p90) cc_final: 0.3395 (p90) outliers start: 13 outliers final: 7 residues processed: 158 average time/residue: 0.0764 time to fit residues: 16.9954 Evaluate side-chains 159 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 25 optimal weight: 0.5980 chunk 88 optimal weight: 0.1980 chunk 57 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 29 optimal weight: 0.0050 chunk 106 optimal weight: 7.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.176397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.150134 restraints weight = 10756.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154146 restraints weight = 5975.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.156815 restraints weight = 3995.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.158597 restraints weight = 3027.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159638 restraints weight = 2477.423| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.1550 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= 0.115 Angle : 0.516 9.616 10735 Z= 0.272 Chirality : 0.041 0.159 1273 Planarity : 0.004 0.050 1400 Dihedral : 4.250 26.315 1125 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.79 % Allowed : 16.62 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.26), residues: 1057 helix: 0.74 (0.28), residues: 369 sheet: -1.31 (0.43), residues: 140 loop : -1.61 (0.26), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 499 TYR 0.019 0.001 TYR A 879 PHE 0.021 0.001 PHE A 957 TRP 0.008 0.001 TRP A 623 HIS 0.005 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7910) covalent geometry : angle 0.51616 (10735) hydrogen bonds : bond 0.03562 ( 318) hydrogen bonds : angle 5.30729 ( 924) *********************** 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 159 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 121 LYS cc_start: 0.7844 (mtmt) cc_final: 0.7511 (mtmt) REVERT: A 153 CYS cc_start: 0.6585 (t) cc_final: 0.6301 (t) REVERT: A 229 LYS cc_start: 0.7649 (mttm) cc_final: 0.7373 (mttp) REVERT: A 282 LEU cc_start: 0.7534 (mt) cc_final: 0.7232 (mt) REVERT: A 346 ASP cc_start: 0.6487 (p0) cc_final: 0.6236 (p0) REVERT: A 355 MET cc_start: 0.4770 (tpt) cc_final: 0.4512 (tpt) REVERT: A 424 ASP cc_start: 0.7249 (p0) cc_final: 0.6981 (p0) REVERT: A 478 GLN cc_start: 0.7569 (tt0) cc_final: 0.7226 (tt0) REVERT: A 663 MET cc_start: 0.8314 (ptm) cc_final: 0.8066 (ttp) REVERT: A 883 ASP cc_start: 0.7990 (t70) cc_final: 0.7536 (t0) REVERT: A 907 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7594 (mtmt) REVERT: A 923 LYS cc_start: 0.7663 (mtmm) cc_final: 0.7333 (mtmm) REVERT: A 957 PHE cc_start: 0.5320 (p90) cc_final: 0.3332 (p90) outliers start: 6 outliers final: 2 residues processed: 155 average time/residue: 0.0830 time to fit residues: 18.0116 Evaluate side-chains 151 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 ASP 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 8 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 51 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.174225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.147271 restraints weight = 11036.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151406 restraints weight = 6175.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.154119 restraints weight = 4130.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155806 restraints weight = 3137.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.157003 restraints weight = 2588.967| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 moved from start: 0.1930 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= 0.209 Angle : 0.590 8.735 10735 Z= 0.312 Chirality : 0.044 0.168 1273 Planarity : 0.004 0.052 1400 Dihedral : 4.556 19.174 1124 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 2.24 % Allowed : 17.81 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.25), residues: 1057 helix: 0.60 (0.28), residues: 373 sheet: -1.47 (0.43), residues: 145 loop : -1.77 (0.25), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 194 TYR 0.023 0.002 TYR A 879 PHE 0.023 0.002 PHE A 471 TRP 0.015 0.002 TRP A 485 HIS 0.007 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 7910) covalent geometry : angle 0.59009 (10735) hydrogen bonds : bond 0.03999 ( 318) hydrogen bonds : angle 5.44308 ( 924) *********************** 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 167 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5392 (tt0) cc_final: 0.5186 (tt0) REVERT: A 239 LEU cc_start: 0.8019 (mt) cc_final: 0.7804 (mt) REVERT: A 282 LEU cc_start: 0.7574 (mt) cc_final: 0.7331 (mt) REVERT: A 328 GLU cc_start: 0.6717 (mp0) cc_final: 0.6323 (mp0) REVERT: A 346 ASP cc_start: 0.6541 (p0) cc_final: 0.6189 (p0) REVERT: A 355 MET cc_start: 0.4858 (tpt) cc_final: 0.4511 (tpt) REVERT: A 424 ASP cc_start: 0.7312 (p0) cc_final: 0.6991 (p0) REVERT: A 663 MET cc_start: 0.8354 (ptm) cc_final: 0.8100 (ttp) REVERT: A 724 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8125 (tp) REVERT: A 883 ASP cc_start: 0.8031 (t70) cc_final: 0.7592 (t0) REVERT: A 907 LYS cc_start: 0.8046 (mtmt) cc_final: 0.7694 (mtmt) REVERT: A 923 LYS cc_start: 0.7744 (mtmm) cc_final: 0.7406 (mtmm) REVERT: A 957 PHE cc_start: 0.5567 (p90) cc_final: 0.3679 (p90) outliers start: 17 outliers final: 9 residues processed: 160 average time/residue: 0.0718 time to fit residues: 16.1084 Evaluate side-chains 164 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 268 ASP Chi-restraints excluded: chain A residue 271 THR 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 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 24 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 40 optimal weight: 0.0670 chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 93 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.175158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148699 restraints weight = 10920.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152790 restraints weight = 6044.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155477 restraints weight = 4035.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157066 restraints weight = 3049.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158334 restraints weight = 2530.654| |-----------------------------------------------------------------------------| r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7910 Z= 0.137 Angle : 0.547 11.453 10735 Z= 0.285 Chirality : 0.042 0.170 1273 Planarity : 0.004 0.065 1400 Dihedral : 4.275 18.065 1124 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.76 % Favored : 92.15 % Rotamer: Outliers : 1.72 % Allowed : 19.66 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 1057 helix: 0.80 (0.28), residues: 367 sheet: -1.43 (0.42), residues: 145 loop : -1.73 (0.25), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 720 TYR 0.022 0.001 TYR A 879 PHE 0.021 0.001 PHE A 957 TRP 0.010 0.001 TRP A 623 HIS 0.011 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7910) covalent geometry : angle 0.54673 (10735) hydrogen bonds : bond 0.03398 ( 318) hydrogen bonds : angle 5.19537 ( 924) *********************** 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 163 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.323 Fit side-chains REVERT: A 223 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7776 (m) REVERT: A 239 LEU cc_start: 0.7989 (mt) cc_final: 0.7729 (mt) REVERT: A 282 LEU cc_start: 0.7567 (mt) cc_final: 0.7349 (mt) REVERT: A 328 GLU cc_start: 0.6666 (mp0) cc_final: 0.6284 (mp0) REVERT: A 346 ASP cc_start: 0.6468 (p0) cc_final: 0.6216 (p0) REVERT: A 355 MET cc_start: 0.4739 (tpt) cc_final: 0.4421 (tpt) REVERT: A 424 ASP cc_start: 0.7243 (p0) cc_final: 0.6960 (p0) REVERT: A 663 MET cc_start: 0.8328 (ptm) cc_final: 0.8115 (ttp) REVERT: A 880 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6273 (mpp) REVERT: A 883 ASP cc_start: 0.8022 (t70) cc_final: 0.7569 (t0) REVERT: A 897 ASP cc_start: 0.7822 (m-30) cc_final: 0.7353 (m-30) REVERT: A 923 LYS cc_start: 0.7689 (mtmm) cc_final: 0.7376 (mtmm) REVERT: A 935 LYS cc_start: 0.8217 (mmmm) cc_final: 0.8003 (mmmm) REVERT: A 957 PHE cc_start: 0.5561 (p90) cc_final: 0.3626 (p90) outliers start: 13 outliers final: 8 residues processed: 155 average time/residue: 0.0821 time to fit residues: 17.7880 Evaluate side-chains 155 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 145 time to evaluate : 0.182 ------------------------------------------------------------------------------- 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 414 ASP Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 773 SER 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 93 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.170931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144188 restraints weight = 10960.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148162 restraints weight = 6184.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.150909 restraints weight = 4134.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.152439 restraints weight = 3120.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153876 restraints weight = 2603.431| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 7910 Z= 0.360 Angle : 0.717 9.774 10735 Z= 0.384 Chirality : 0.049 0.168 1273 Planarity : 0.005 0.058 1400 Dihedral : 5.272 21.926 1124 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.46 % Favored : 90.44 % Rotamer: Outliers : 3.30 % Allowed : 19.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.25), residues: 1057 helix: 0.10 (0.27), residues: 371 sheet: -1.65 (0.41), residues: 157 loop : -2.02 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 194 TYR 0.030 0.003 TYR A 879 PHE 0.030 0.003 PHE A 471 TRP 0.024 0.003 TRP A 485 HIS 0.010 0.002 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00786 ( 7910) covalent geometry : angle 0.71738 (10735) hydrogen bonds : bond 0.04715 ( 318) hydrogen bonds : angle 5.78804 ( 924) *********************** 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 179 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 0.263 Fit side-chains REVERT: A 109 ILE cc_start: 0.7862 (pt) cc_final: 0.7659 (pt) REVERT: A 239 LEU cc_start: 0.7995 (mt) cc_final: 0.7659 (mt) REVERT: A 282 LEU cc_start: 0.7595 (mt) cc_final: 0.7375 (mt) REVERT: A 328 GLU cc_start: 0.6740 (mp0) cc_final: 0.6346 (mp0) REVERT: A 346 ASP cc_start: 0.6582 (p0) cc_final: 0.6291 (p0) REVERT: A 354 GLN cc_start: 0.6783 (mm-40) cc_final: 0.6467 (mt0) REVERT: A 355 MET cc_start: 0.4766 (tpt) cc_final: 0.4489 (tpt) REVERT: A 424 ASP cc_start: 0.7228 (p0) cc_final: 0.6939 (p0) REVERT: A 724 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8130 (tp) REVERT: A 731 LEU cc_start: 0.7835 (mt) cc_final: 0.7518 (mp) REVERT: A 869 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6533 (mt) REVERT: A 880 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6403 (mpp) REVERT: A 883 ASP cc_start: 0.8100 (t70) cc_final: 0.7605 (t0) REVERT: A 897 ASP cc_start: 0.7862 (m-30) cc_final: 0.7304 (m-30) REVERT: A 907 LYS cc_start: 0.8132 (mtmt) cc_final: 0.7734 (mtmt) REVERT: A 923 LYS cc_start: 0.7807 (mtmm) cc_final: 0.7458 (mtmm) REVERT: A 935 LYS cc_start: 0.8219 (mmmm) cc_final: 0.7998 (mmmm) REVERT: A 957 PHE cc_start: 0.5753 (p90) cc_final: 0.3882 (p90) outliers start: 25 outliers final: 16 residues processed: 168 average time/residue: 0.0711 time to fit residues: 16.6794 Evaluate side-chains 175 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 164 ILE Chi-restraints excluded: chain A residue 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 414 ASP Chi-restraints excluded: chain A residue 463 THR Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 525 SER 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 1.9990 chunk 86 optimal weight: 0.0020 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 88 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.175010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.148808 restraints weight = 10945.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.152855 restraints weight = 6054.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155262 restraints weight = 4033.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.157326 restraints weight = 3089.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158319 restraints weight = 2516.402| |-----------------------------------------------------------------------------| r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2311 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= 0.126 Angle : 0.546 8.812 10735 Z= 0.289 Chirality : 0.041 0.163 1273 Planarity : 0.004 0.050 1400 Dihedral : 4.456 19.478 1124 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.19 % Favored : 92.72 % Rotamer: Outliers : 2.37 % Allowed : 20.32 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.26), residues: 1057 helix: 0.65 (0.28), residues: 367 sheet: -1.35 (0.45), residues: 140 loop : -1.84 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 898 TYR 0.021 0.001 TYR A 879 PHE 0.023 0.001 PHE A 957 TRP 0.013 0.001 TRP A 623 HIS 0.008 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7910) covalent geometry : angle 0.54573 (10735) hydrogen bonds : bond 0.03249 ( 318) hydrogen bonds : angle 5.14767 ( 924) *********************** 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 168 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5527 (tt0) cc_final: 0.5202 (tt0) REVERT: A 239 LEU cc_start: 0.7997 (mt) cc_final: 0.7739 (mt) REVERT: A 282 LEU cc_start: 0.7572 (mt) cc_final: 0.7367 (mt) REVERT: A 328 GLU cc_start: 0.6678 (mp0) cc_final: 0.6300 (mp0) REVERT: A 355 MET cc_start: 0.4700 (tpt) cc_final: 0.4435 (tpt) REVERT: A 424 ASP cc_start: 0.7129 (p0) cc_final: 0.6858 (p0) REVERT: A 724 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 869 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6217 (mt) REVERT: A 880 MET cc_start: 0.7058 (OUTLIER) cc_final: 0.6171 (mpp) REVERT: A 883 ASP cc_start: 0.8056 (t70) cc_final: 0.7543 (t0) REVERT: A 923 LYS cc_start: 0.7693 (mtmm) cc_final: 0.7379 (mtmm) REVERT: A 957 PHE cc_start: 0.5663 (p90) cc_final: 0.3681 (p90) outliers start: 18 outliers final: 10 residues processed: 161 average time/residue: 0.0746 time to fit residues: 16.5998 Evaluate side-chains 161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 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 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 45 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 chunk 72 optimal weight: 0.0030 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 GLN A 835 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.174816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.148383 restraints weight = 10970.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.152417 restraints weight = 6104.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155093 restraints weight = 4078.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157042 restraints weight = 3082.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.157754 restraints weight = 2511.071| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.2393 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= 0.139 Angle : 0.554 9.174 10735 Z= 0.292 Chirality : 0.042 0.163 1273 Planarity : 0.004 0.049 1400 Dihedral : 4.364 19.404 1124 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.39 % Rotamer: Outliers : 1.98 % Allowed : 21.77 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.26), residues: 1057 helix: 0.71 (0.28), residues: 368 sheet: -1.42 (0.43), residues: 145 loop : -1.80 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 898 TYR 0.024 0.002 TYR A 879 PHE 0.020 0.002 PHE A 957 TRP 0.012 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 7910) covalent geometry : angle 0.55407 (10735) hydrogen bonds : bond 0.03307 ( 318) hydrogen bonds : angle 5.08910 ( 924) *********************** 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 165 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 GLU cc_start: 0.5438 (tt0) cc_final: 0.5134 (tt0) REVERT: A 239 LEU cc_start: 0.8010 (mt) cc_final: 0.7755 (mt) REVERT: A 328 GLU cc_start: 0.6701 (mp0) cc_final: 0.6302 (mp0) REVERT: A 355 MET cc_start: 0.4701 (tpt) cc_final: 0.4419 (tpt) REVERT: A 424 ASP cc_start: 0.7196 (p0) cc_final: 0.6919 (p0) REVERT: A 478 GLN cc_start: 0.7576 (tt0) cc_final: 0.7088 (tt0) REVERT: A 762 GLN cc_start: 0.8409 (mp10) cc_final: 0.7937 (mp10) REVERT: A 869 LEU cc_start: 0.6545 (OUTLIER) cc_final: 0.6222 (mt) REVERT: A 880 MET cc_start: 0.7076 (OUTLIER) cc_final: 0.6233 (mpp) REVERT: A 883 ASP cc_start: 0.8066 (t70) cc_final: 0.7562 (t0) REVERT: A 923 LYS cc_start: 0.7695 (mtmm) cc_final: 0.7367 (mtmm) REVERT: A 957 PHE cc_start: 0.5643 (p90) cc_final: 0.3663 (p90) outliers start: 15 outliers final: 11 residues processed: 158 average time/residue: 0.0701 time to fit residues: 15.4752 Evaluate side-chains 161 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.191 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 880 MET Chi-restraints excluded: chain A residue 959 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 48 optimal weight: 0.0970 chunk 18 optimal weight: 10.0000 chunk 72 optimal weight: 0.2980 chunk 44 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 0.0670 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN A 824 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.176517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.150276 restraints weight = 10901.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154311 restraints weight = 6093.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.156978 restraints weight = 4072.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.158586 restraints weight = 3083.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.159858 restraints weight = 2560.154| |-----------------------------------------------------------------------------| r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7910 Z= 0.112 Angle : 0.559 11.176 10735 Z= 0.285 Chirality : 0.041 0.159 1273 Planarity : 0.004 0.050 1400 Dihedral : 4.173 19.754 1124 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.57 % Favored : 92.24 % Rotamer: Outliers : 1.72 % Allowed : 22.69 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.26), residues: 1057 helix: 0.83 (0.28), residues: 370 sheet: -1.37 (0.42), residues: 147 loop : -1.73 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 898 TYR 0.024 0.001 TYR A 879 PHE 0.024 0.001 PHE A 957 TRP 0.012 0.001 TRP A 623 HIS 0.008 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7910) covalent geometry : angle 0.55926 (10735) hydrogen bonds : bond 0.03056 ( 318) hydrogen bonds : angle 4.91531 ( 924) *********************** 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 163 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 THR cc_start: 0.7730 (t) cc_final: 0.7412 (m) REVERT: A 239 LEU cc_start: 0.7990 (mt) cc_final: 0.7715 (mt) REVERT: A 328 GLU cc_start: 0.6677 (mp0) cc_final: 0.6269 (mp0) REVERT: A 355 MET cc_start: 0.4696 (tpt) cc_final: 0.4441 (tpt) REVERT: A 424 ASP cc_start: 0.7181 (p0) cc_final: 0.6906 (p0) REVERT: A 688 LYS cc_start: 0.7437 (mptt) cc_final: 0.6738 (mptt) REVERT: A 762 GLN cc_start: 0.8367 (mp10) cc_final: 0.7904 (mp10) REVERT: A 869 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.6186 (mt) REVERT: A 880 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6178 (mpp) REVERT: A 883 ASP cc_start: 0.8064 (t70) cc_final: 0.7576 (t0) REVERT: A 923 LYS cc_start: 0.7662 (mtmm) cc_final: 0.7338 (mtmm) REVERT: A 957 PHE cc_start: 0.5531 (p90) cc_final: 0.3482 (p90) outliers start: 13 outliers final: 9 residues processed: 156 average time/residue: 0.0803 time to fit residues: 17.5177 Evaluate side-chains 155 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 880 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 713 GLN A 835 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.175090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.148784 restraints weight = 10928.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152768 restraints weight = 6141.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.155417 restraints weight = 4122.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.157025 restraints weight = 3115.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.158414 restraints weight = 2607.231| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7910 Z= 0.152 Angle : 0.594 11.212 10735 Z= 0.306 Chirality : 0.043 0.181 1273 Planarity : 0.004 0.050 1400 Dihedral : 4.296 19.530 1124 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.51 % Favored : 91.30 % Rotamer: Outliers : 1.72 % Allowed : 22.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.26), residues: 1057 helix: 0.83 (0.28), residues: 368 sheet: -1.34 (0.42), residues: 145 loop : -1.78 (0.26), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 898 TYR 0.034 0.002 TYR A 345 PHE 0.021 0.002 PHE A 471 TRP 0.011 0.001 TRP A 623 HIS 0.009 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7910) covalent geometry : angle 0.59428 (10735) hydrogen bonds : bond 0.03337 ( 318) hydrogen bonds : angle 5.02239 ( 924) ********************** 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 152 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 239 LEU cc_start: 0.8001 (mt) cc_final: 0.7746 (mt) REVERT: A 247 MET cc_start: 0.4918 (mmp) cc_final: 0.3859 (mmp) REVERT: A 355 MET cc_start: 0.4720 (tpt) cc_final: 0.4432 (tpt) REVERT: A 424 ASP cc_start: 0.7242 (p0) cc_final: 0.6964 (p0) REVERT: A 762 GLN cc_start: 0.8391 (mp10) cc_final: 0.7923 (mp10) REVERT: A 869 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6226 (mt) REVERT: A 880 MET cc_start: 0.7127 (OUTLIER) cc_final: 0.6257 (mpp) REVERT: A 883 ASP cc_start: 0.8087 (t70) cc_final: 0.7604 (t0) REVERT: A 897 ASP cc_start: 0.7923 (m-30) cc_final: 0.7415 (m-30) REVERT: A 923 LYS cc_start: 0.7711 (mtmm) cc_final: 0.7402 (mtmm) REVERT: A 957 PHE cc_start: 0.5574 (p90) cc_final: 0.3536 (p90) outliers start: 13 outliers final: 10 residues processed: 145 average time/residue: 0.0663 time to fit residues: 13.7292 Evaluate side-chains 147 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 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 525 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 794 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 880 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 94 optimal weight: 20.0000 chunk 56 optimal weight: 4.9990 chunk 70 optimal weight: 0.0070 chunk 103 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- 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 570 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.173429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147112 restraints weight = 10937.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.151130 restraints weight = 6156.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.153730 restraints weight = 4112.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155513 restraints weight = 3110.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.156223 restraints weight = 2550.610| |-----------------------------------------------------------------------------| r_work (final): 0.3868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 7910 Z= 0.208 Angle : 0.640 11.309 10735 Z= 0.333 Chirality : 0.045 0.165 1273 Planarity : 0.004 0.050 1400 Dihedral : 4.608 19.863 1124 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.08 % Favored : 90.73 % Rotamer: Outliers : 2.11 % Allowed : 22.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.26), residues: 1057 helix: 0.54 (0.27), residues: 373 sheet: -1.38 (0.43), residues: 145 loop : -1.85 (0.26), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 898 TYR 0.036 0.002 TYR A 345 PHE 0.025 0.002 PHE A 471 TRP 0.014 0.002 TRP A 485 HIS 0.010 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00461 ( 7910) covalent geometry : angle 0.64030 (10735) hydrogen bonds : bond 0.03774 ( 318) hydrogen bonds : angle 5.27381 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1764.71 seconds wall clock time: 30 minutes 57.39 seconds (1857.39 seconds total)