Starting phenix.real_space_refine on Tue Feb 3 20:09:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmb_61596/02_2026/9jmb_61596_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmb_61596/02_2026/9jmb_61596.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jmb_61596/02_2026/9jmb_61596_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmb_61596/02_2026/9jmb_61596_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jmb_61596/02_2026/9jmb_61596.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmb_61596/02_2026/9jmb_61596.map" } resolution = 2.18 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= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 4125 2.51 5 N 1118 2.21 5 O 1240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s 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: 6512 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4713 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 557} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 975 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Time building chain proxies: 1.51, per 1000 atoms: 0.23 Number of scatterers: 6512 At special positions: 0 Unit cell: (109.2, 112.45, 180.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 1240 8.00 N 1118 7.00 C 4125 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 111 " - pdb=" SG CYS A 570 " distance=2.02 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 526 " distance=2.04 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 266 " distance=2.04 Simple disulfide: pdb=" SG CYS A 359 " - pdb=" SG CYS A 407 " distance=2.02 Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.05 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: 0.57 Conformation dependent library (CDL) restraints added in 249.9 milliseconds 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1534 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 17 sheets defined 17.6% alpha, 43.4% 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 188 through 195 Processing helix chain 'A' and resid 195 through 200 Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.700A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.521A pdb=" N VAL A 402 " --> pdb=" O LEU A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 421 removed outlier: 3.906A pdb=" N ARG A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 532 removed outlier: 3.548A pdb=" N HIS A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 543 removed outlier: 4.065A pdb=" N LYS A 541 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A 542 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 4.084A pdb=" N GLY A 553 " --> pdb=" O SER A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 694 Processing helix chain 'A' and resid 698 through 707 Processing helix chain 'A' and resid 708 through 714 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.502A pdb=" N ASP H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.502A pdb=" N LYS H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA2, first strand: chain 'A' and resid 388 through 392 removed outlier: 6.536A pdb=" N TRP A 364 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS A 146 " --> pdb=" O TRP A 364 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU A 366 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 144 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP A 368 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA A 142 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 13.920A pdb=" N TYR A 137 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N SER A 452 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU A 139 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 388 through 392 removed outlier: 6.536A pdb=" N TRP A 364 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N LYS A 146 " --> pdb=" O TRP A 364 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N GLU A 366 " --> pdb=" O VAL A 144 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N VAL A 144 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ASP A 368 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ALA A 142 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 13.920A pdb=" N TYR A 137 " --> pdb=" O SER A 452 " (cutoff:3.500A) removed outlier: 9.551A pdb=" N SER A 452 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU A 139 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 186 removed outlier: 6.459A pdb=" N GLN A 167 " --> pdb=" O MET A 178 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 180 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N VAL A 165 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU A 182 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N VAL A 163 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ARG A 184 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS A 161 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N TYR A 159 " --> pdb=" O PRO A 186 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 231 removed outlier: 7.530A pdb=" N LYS A 155 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ASP A 350 " --> pdb=" O LYS A 155 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR A 335 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 Processing sheet with id=AA7, first strand: chain 'A' and resid 205 through 210 Processing sheet with id=AA8, first strand: chain 'A' and resid 579 through 580 Processing sheet with id=AA9, first strand: chain 'A' and resid 592 through 594 Processing sheet with id=AB1, first strand: chain 'A' and resid 635 through 639 removed outlier: 6.665A pdb=" N TYR A 644 " --> pdb=" O GLN A 655 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLN A 655 " --> pdb=" O TYR A 644 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TYR A 646 " --> pdb=" O SER A 653 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB4, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.784A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR H 111 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.784A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.549A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N THR L 68 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.191A pdb=" N SER L 27 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 10.003A pdb=" N SER L 66 " --> pdb=" O SER L 27 " (cutoff:3.500A) removed outlier: 11.702A pdb=" N VAL L 29 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 12.264A pdb=" N SER L 64 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.423A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLN L 36 " --> pdb=" O PRO L 45 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.423A pdb=" N LEU L 11 " --> pdb=" O GLU L 104 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR L 96 " --> pdb=" O GLN L 89 " (cutoff:3.500A) 284 hydrogen bonds defined for protein. 747 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: 1.10 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2093 1.34 - 1.46: 1770 1.46 - 1.59: 2774 1.59 - 1.72: 0 1.72 - 1.84: 44 Bond restraints: 6681 Sorted by residual: bond pdb=" CB ARG A 337 " pdb=" CG ARG A 337 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.10e+00 bond pdb=" N VAL A 402 " pdb=" CA VAL A 402 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.24e-02 6.50e+03 8.07e+00 bond pdb=" N ARG A 555 " pdb=" CA ARG A 555 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.25e-02 6.40e+03 7.91e+00 bond pdb=" N SER A 398 " pdb=" CA SER A 398 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.25e-02 6.40e+03 6.46e+00 bond pdb=" CA SER A 400 " pdb=" CB SER A 400 " ideal model delta sigma weight residual 1.532 1.487 0.045 1.78e-02 3.16e+03 6.44e+00 ... (remaining 6676 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 8765 2.57 - 5.14: 281 5.14 - 7.70: 20 7.70 - 10.27: 10 10.27 - 12.84: 3 Bond angle restraints: 9079 Sorted by residual: angle pdb=" N LEU A 503 " pdb=" CA LEU A 503 " pdb=" C LEU A 503 " ideal model delta sigma weight residual 112.90 106.38 6.52 1.31e+00 5.83e-01 2.48e+01 angle pdb=" C ARG A 502 " pdb=" CA ARG A 502 " pdb=" CB ARG A 502 " ideal model delta sigma weight residual 109.99 119.64 -9.65 2.09e+00 2.29e-01 2.13e+01 angle pdb=" C ALA L 49 " pdb=" N THR L 50 " pdb=" CA THR L 50 " ideal model delta sigma weight residual 121.54 130.15 -8.61 1.91e+00 2.74e-01 2.03e+01 angle pdb=" CA VAL A 556 " pdb=" C VAL A 556 " pdb=" O VAL A 556 " ideal model delta sigma weight residual 121.64 117.49 4.15 9.80e-01 1.04e+00 1.80e+01 angle pdb=" N SER A 400 " pdb=" CA SER A 400 " pdb=" C SER A 400 " ideal model delta sigma weight residual 113.16 107.96 5.20 1.24e+00 6.50e-01 1.76e+01 ... (remaining 9074 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 3742 17.55 - 35.09: 172 35.09 - 52.64: 44 52.64 - 70.18: 7 70.18 - 87.73: 5 Dihedral angle restraints: 3970 sinusoidal: 1575 harmonic: 2395 Sorted by residual: dihedral pdb=" CD ARG A 401 " pdb=" NE ARG A 401 " pdb=" CZ ARG A 401 " pdb=" NH1 ARG A 401 " ideal model delta sinusoidal sigma weight residual 0.00 87.73 -87.73 1 1.00e+01 1.00e-02 9.22e+01 dihedral pdb=" CB CYS A 593 " pdb=" SG CYS A 593 " pdb=" SG CYS A 630 " pdb=" CB CYS A 630 " ideal model delta sinusoidal sigma weight residual -86.00 -162.33 76.33 1 1.00e+01 1.00e-02 7.33e+01 dihedral pdb=" CB CYS A 111 " pdb=" SG CYS A 111 " pdb=" SG CYS A 570 " pdb=" CB CYS A 570 " ideal model delta sinusoidal sigma weight residual 93.00 157.36 -64.36 1 1.00e+01 1.00e-02 5.45e+01 ... (remaining 3967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 666 0.059 - 0.118: 230 0.118 - 0.177: 61 0.177 - 0.236: 19 0.236 - 0.295: 2 Chirality restraints: 978 Sorted by residual: chirality pdb=" CB ILE L 2 " pdb=" CA ILE L 2 " pdb=" CG1 ILE L 2 " pdb=" CG2 ILE L 2 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL A 681 " pdb=" CA VAL A 681 " pdb=" CG1 VAL A 681 " pdb=" CG2 VAL A 681 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB THR L 101 " pdb=" CA THR L 101 " pdb=" OG1 THR L 101 " pdb=" CG2 THR L 101 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 975 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 401 " 1.097 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 401 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 401 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 401 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 401 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 621 " 0.893 9.50e-02 1.11e+02 4.00e-01 9.72e+01 pdb=" NE ARG A 621 " -0.052 2.00e-02 2.50e+03 pdb=" CZ ARG A 621 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 621 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 621 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 555 " -0.483 9.50e-02 1.11e+02 2.17e-01 2.87e+01 pdb=" NE ARG A 555 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 555 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 555 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 555 " -0.017 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1841 2.81 - 3.34: 5304 3.34 - 3.86: 10681 3.86 - 4.38: 12179 4.38 - 4.90: 20987 Nonbonded interactions: 50992 Sorted by model distance: nonbonded pdb=" OH TYR A 277 " pdb=" OD2 ASP A 403 " model vdw 2.293 3.040 nonbonded pdb=" O GLY A 171 " pdb=" NH2 ARG A 253 " model vdw 2.327 3.120 nonbonded pdb=" O GLY H 113 " pdb=" OG SER L 42 " model vdw 2.327 3.040 nonbonded pdb=" OG SER L 62 " pdb=" OG1 THR L 73 " model vdw 2.347 3.040 nonbonded pdb=" O PHE A 218 " pdb=" OG1 THR A 262 " model vdw 2.363 3.040 ... (remaining 50987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 16.560 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.720 Find NCS groups from input model: 0.020 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:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 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 : 0.009 0.085 6688 Z= 0.413 Angle : 1.069 12.839 9093 Z= 0.613 Chirality : 0.067 0.295 978 Planarity : 0.022 0.492 1173 Dihedral : 11.486 87.729 2415 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.00 % Allowed : 5.83 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -2.46 (0.24), residues: 804 helix: -4.19 (0.25), residues: 99 sheet: -0.75 (0.28), residues: 265 loop : -1.53 (0.23), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 380 TYR 0.023 0.003 TYR A 298 PHE 0.046 0.005 PHE A 379 TRP 0.034 0.004 TRP H 112 HIS 0.029 0.004 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00924 ( 6681) covalent geometry : angle 1.06552 ( 9079) SS BOND : bond 0.00993 ( 7) SS BOND : angle 2.38519 ( 14) hydrogen bonds : bond 0.22386 ( 230) hydrogen bonds : angle 9.35201 ( 747) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 0.259 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 201 average time/residue: 0.6345 time to fit residues: 133.1334 Evaluate side-chains 104 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 431 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS A 537 ASN ** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 HIS L 1 GLN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.104171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.071574 restraints weight = 10685.857| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.29 r_work: 0.2931 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 6688 Z= 0.148 Angle : 0.597 12.135 9093 Z= 0.311 Chirality : 0.045 0.132 978 Planarity : 0.006 0.059 1173 Dihedral : 5.131 40.098 917 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.24 % Favored : 98.63 % Rotamer: Outliers : 3.84 % Allowed : 12.66 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -1.01 (0.26), residues: 804 helix: -1.14 (0.43), residues: 100 sheet: -0.06 (0.30), residues: 273 loop : -0.91 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 635 TYR 0.013 0.002 TYR A 159 PHE 0.019 0.002 PHE A 282 TRP 0.014 0.001 TRP H 112 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6681) covalent geometry : angle 0.58866 ( 9079) SS BOND : bond 0.00589 ( 7) SS BOND : angle 2.58564 ( 14) hydrogen bonds : bond 0.04248 ( 230) hydrogen bonds : angle 5.61218 ( 747) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.250 Fit side-chains REVERT: A 172 HIS cc_start: 0.8430 (t70) cc_final: 0.8037 (t70) REVERT: A 431 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8756 (m) REVERT: A 701 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8504 (mm-30) REVERT: H 19 LYS cc_start: 0.8923 (OUTLIER) cc_final: 0.8690 (tttp) REVERT: H 46 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8560 (tt0) REVERT: L 60 ARG cc_start: 0.8340 (ptt-90) cc_final: 0.8115 (ptt-90) REVERT: L 78 GLU cc_start: 0.7582 (mp0) cc_final: 0.7171 (mp0) outliers start: 27 outliers final: 6 residues processed: 118 average time/residue: 0.6297 time to fit residues: 77.8294 Evaluate side-chains 93 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain H residue 19 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.102376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.069407 restraints weight = 10750.229| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.29 r_work: 0.2888 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 6688 Z= 0.155 Angle : 0.554 9.990 9093 Z= 0.294 Chirality : 0.045 0.174 978 Planarity : 0.005 0.044 1173 Dihedral : 4.847 42.140 916 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.56 % Allowed : 13.23 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -0.16 (0.28), residues: 804 helix: 0.71 (0.51), residues: 100 sheet: 0.23 (0.30), residues: 285 loop : -0.47 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 24 TYR 0.011 0.001 TYR A 424 PHE 0.019 0.002 PHE A 282 TRP 0.015 0.001 TRP L 90 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 6681) covalent geometry : angle 0.54633 ( 9079) SS BOND : bond 0.00339 ( 7) SS BOND : angle 2.42583 ( 14) hydrogen bonds : bond 0.03991 ( 230) hydrogen bonds : angle 5.24289 ( 747) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 431 VAL cc_start: 0.8962 (OUTLIER) cc_final: 0.8757 (m) REVERT: A 620 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8275 (mt) REVERT: A 635 ARG cc_start: 0.8439 (ttp-110) cc_final: 0.7817 (mtp-110) REVERT: A 701 GLU cc_start: 0.8693 (mm-30) cc_final: 0.8465 (mm-30) REVERT: H 46 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8598 (tt0) REVERT: L 2 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7932 (mm) REVERT: L 60 ARG cc_start: 0.8320 (ptt-90) cc_final: 0.8113 (ptt-90) REVERT: L 78 GLU cc_start: 0.7502 (mp0) cc_final: 0.7104 (mp0) outliers start: 25 outliers final: 11 residues processed: 102 average time/residue: 0.5363 time to fit residues: 57.6881 Evaluate side-chains 96 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 68 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.103356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.070525 restraints weight = 10783.303| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.28 r_work: 0.2909 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6688 Z= 0.110 Angle : 0.502 8.994 9093 Z= 0.266 Chirality : 0.043 0.155 978 Planarity : 0.004 0.041 1173 Dihedral : 4.545 40.661 916 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.41 % Allowed : 13.94 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.28 (0.28), residues: 804 helix: 1.52 (0.53), residues: 100 sheet: 0.46 (0.30), residues: 284 loop : -0.27 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.017 0.001 TYR A 652 PHE 0.016 0.001 PHE A 282 TRP 0.014 0.001 TRP L 90 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6681) covalent geometry : angle 0.49815 ( 9079) SS BOND : bond 0.00333 ( 7) SS BOND : angle 1.69591 ( 14) hydrogen bonds : bond 0.03410 ( 230) hydrogen bonds : angle 4.86840 ( 747) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.250 Fit side-chains revert: symmetry clash REVERT: A 620 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8222 (mt) REVERT: A 635 ARG cc_start: 0.8415 (ttp-110) cc_final: 0.7815 (mtp-110) REVERT: A 701 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8488 (mm-30) REVERT: H 23 LYS cc_start: 0.8794 (tppp) cc_final: 0.8545 (tttm) REVERT: H 82 GLU cc_start: 0.8371 (tp30) cc_final: 0.8088 (tp30) REVERT: L 78 GLU cc_start: 0.7436 (mp0) cc_final: 0.6929 (mp0) outliers start: 24 outliers final: 11 residues processed: 103 average time/residue: 0.5285 time to fit residues: 57.5408 Evaluate side-chains 99 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 40 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.100619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.067032 restraints weight = 10940.652| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.32 r_work: 0.2835 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6688 Z= 0.183 Angle : 0.553 8.260 9093 Z= 0.294 Chirality : 0.045 0.146 978 Planarity : 0.005 0.042 1173 Dihedral : 4.785 44.456 915 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.41 % Allowed : 14.08 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.39 (0.29), residues: 804 helix: 1.56 (0.53), residues: 100 sheet: 0.58 (0.30), residues: 284 loop : -0.23 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.013 0.002 TYR A 652 PHE 0.020 0.002 PHE A 282 TRP 0.016 0.001 TRP L 90 HIS 0.006 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00432 ( 6681) covalent geometry : angle 0.54867 ( 9079) SS BOND : bond 0.00408 ( 7) SS BOND : angle 1.75801 ( 14) hydrogen bonds : bond 0.03979 ( 230) hydrogen bonds : angle 5.08230 ( 747) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.280 Fit side-chains revert: symmetry clash REVERT: A 620 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 635 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.7791 (mtp-110) REVERT: A 701 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8478 (mm-30) REVERT: H 23 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8521 (tttm) REVERT: H 54 TYR cc_start: 0.8728 (t80) cc_final: 0.8189 (t80) REVERT: H 82 GLU cc_start: 0.8428 (tp30) cc_final: 0.8160 (tp30) REVERT: H 84 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7407 (ptt-90) REVERT: L 103 LEU cc_start: 0.8702 (tp) cc_final: 0.8462 (tm) outliers start: 24 outliers final: 15 residues processed: 101 average time/residue: 0.4983 time to fit residues: 53.1820 Evaluate side-chains 99 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 89 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.099666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.066529 restraints weight = 10750.030| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.29 r_work: 0.2832 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8935 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 6688 Z= 0.236 Angle : 0.587 8.141 9093 Z= 0.314 Chirality : 0.047 0.147 978 Planarity : 0.005 0.044 1173 Dihedral : 4.971 45.989 915 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.70 % Allowed : 14.94 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.39 (0.29), residues: 804 helix: 1.55 (0.53), residues: 100 sheet: 0.60 (0.30), residues: 285 loop : -0.24 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 24 TYR 0.015 0.002 TYR A 650 PHE 0.022 0.002 PHE A 282 TRP 0.021 0.002 TRP L 90 HIS 0.008 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00559 ( 6681) covalent geometry : angle 0.58347 ( 9079) SS BOND : bond 0.00464 ( 7) SS BOND : angle 1.79558 ( 14) hydrogen bonds : bond 0.04283 ( 230) hydrogen bonds : angle 5.18855 ( 747) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: A 620 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 701 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8514 (mm-30) REVERT: H 23 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8580 (tttm) REVERT: H 54 TYR cc_start: 0.8765 (t80) cc_final: 0.8233 (t80) REVERT: H 63 LYS cc_start: 0.8969 (ttmm) cc_final: 0.8737 (ttmt) REVERT: L 78 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: L 103 LEU cc_start: 0.8746 (tp) cc_final: 0.8421 (tm) outliers start: 26 outliers final: 17 residues processed: 97 average time/residue: 0.4508 time to fit residues: 46.2078 Evaluate side-chains 100 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain L residue 78 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 47 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3558 r_free = 0.3558 target = 0.101592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.068734 restraints weight = 10644.890| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.27 r_work: 0.2874 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6688 Z= 0.119 Angle : 0.498 8.144 9093 Z= 0.266 Chirality : 0.043 0.146 978 Planarity : 0.004 0.042 1173 Dihedral : 4.575 43.415 915 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.84 % Allowed : 15.50 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.58 (0.29), residues: 804 helix: 1.98 (0.54), residues: 100 sheet: 0.69 (0.30), residues: 285 loop : -0.17 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 24 TYR 0.013 0.001 TYR A 650 PHE 0.017 0.001 PHE A 282 TRP 0.014 0.001 TRP L 90 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6681) covalent geometry : angle 0.49491 ( 9079) SS BOND : bond 0.00368 ( 7) SS BOND : angle 1.38557 ( 14) hydrogen bonds : bond 0.03439 ( 230) hydrogen bonds : angle 4.86768 ( 747) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 0.199 Fit side-chains REVERT: A 620 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8285 (mt) REVERT: A 701 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8506 (mm-30) REVERT: H 23 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8581 (tttm) REVERT: H 54 TYR cc_start: 0.8731 (t80) cc_final: 0.8205 (t80) outliers start: 20 outliers final: 13 residues processed: 99 average time/residue: 0.4551 time to fit residues: 47.5099 Evaluate side-chains 98 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 568 SER Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 60 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3545 r_free = 0.3545 target = 0.101000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.067590 restraints weight = 10728.128| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.29 r_work: 0.2866 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6688 Z= 0.135 Angle : 0.515 7.571 9093 Z= 0.274 Chirality : 0.043 0.144 978 Planarity : 0.004 0.042 1173 Dihedral : 4.582 43.621 915 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.56 % Allowed : 15.65 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.66 (0.29), residues: 804 helix: 2.02 (0.54), residues: 100 sheet: 0.73 (0.30), residues: 283 loop : -0.09 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 24 TYR 0.017 0.001 TYR A 650 PHE 0.018 0.001 PHE A 282 TRP 0.015 0.001 TRP L 90 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6681) covalent geometry : angle 0.51258 ( 9079) SS BOND : bond 0.00387 ( 7) SS BOND : angle 1.36331 ( 14) hydrogen bonds : bond 0.03557 ( 230) hydrogen bonds : angle 4.89658 ( 747) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.195 Fit side-chains REVERT: A 620 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8243 (mt) REVERT: A 701 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8488 (mm-30) REVERT: H 23 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8543 (tttm) REVERT: H 54 TYR cc_start: 0.8739 (t80) cc_final: 0.8202 (t80) REVERT: L 60 ARG cc_start: 0.8197 (ptt-90) cc_final: 0.7978 (ptt-90) REVERT: L 78 GLU cc_start: 0.7360 (mp0) cc_final: 0.7029 (mp0) REVERT: L 103 LEU cc_start: 0.8694 (tp) cc_final: 0.8303 (tt) outliers start: 18 outliers final: 14 residues processed: 98 average time/residue: 0.4366 time to fit residues: 45.2709 Evaluate side-chains 98 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 66 optimal weight: 6.9990 chunk 3 optimal weight: 0.0770 chunk 73 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.102065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.069019 restraints weight = 10784.480| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.29 r_work: 0.2881 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6688 Z= 0.115 Angle : 0.490 7.044 9093 Z= 0.261 Chirality : 0.043 0.144 978 Planarity : 0.004 0.041 1173 Dihedral : 4.459 42.561 915 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.99 % Allowed : 16.22 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.77 (0.29), residues: 804 helix: 2.13 (0.54), residues: 100 sheet: 0.78 (0.30), residues: 283 loop : -0.00 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 24 TYR 0.017 0.001 TYR A 650 PHE 0.017 0.001 PHE A 282 TRP 0.014 0.001 TRP L 90 HIS 0.004 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6681) covalent geometry : angle 0.48745 ( 9079) SS BOND : bond 0.00388 ( 7) SS BOND : angle 1.26732 ( 14) hydrogen bonds : bond 0.03304 ( 230) hydrogen bonds : angle 4.78089 ( 747) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.182 Fit side-chains REVERT: A 599 VAL cc_start: 0.9183 (t) cc_final: 0.8781 (p) REVERT: A 620 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8210 (mp) REVERT: H 19 LYS cc_start: 0.9063 (tttp) cc_final: 0.8593 (ttmt) REVERT: H 23 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8579 (tttm) REVERT: H 54 TYR cc_start: 0.8722 (t80) cc_final: 0.8180 (t80) REVERT: L 60 ARG cc_start: 0.8188 (ptt-90) cc_final: 0.7946 (ptt-90) REVERT: L 78 GLU cc_start: 0.7383 (mp0) cc_final: 0.7078 (mp0) REVERT: L 103 LEU cc_start: 0.8692 (tp) cc_final: 0.8345 (tt) outliers start: 21 outliers final: 12 residues processed: 102 average time/residue: 0.4882 time to fit residues: 52.6195 Evaluate side-chains 97 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 45 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.099608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.066209 restraints weight = 10685.645| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.27 r_work: 0.2839 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 6688 Z= 0.203 Angle : 0.561 7.067 9093 Z= 0.298 Chirality : 0.046 0.143 978 Planarity : 0.004 0.043 1173 Dihedral : 4.805 45.449 915 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.56 % Allowed : 16.64 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.67 (0.29), residues: 804 helix: 1.87 (0.53), residues: 100 sheet: 0.70 (0.30), residues: 283 loop : -0.01 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 24 TYR 0.016 0.002 TYR A 650 PHE 0.021 0.002 PHE A 282 TRP 0.015 0.002 TRP L 90 HIS 0.007 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 6681) covalent geometry : angle 0.55786 ( 9079) SS BOND : bond 0.00500 ( 7) SS BOND : angle 1.50599 ( 14) hydrogen bonds : bond 0.03974 ( 230) hydrogen bonds : angle 5.06763 ( 747) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1608 Ramachandran restraints generated. 804 Oldfield, 0 Emsley, 804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 620 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8227 (mp) REVERT: H 23 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8516 (tttm) REVERT: H 54 TYR cc_start: 0.8773 (t80) cc_final: 0.8216 (t80) REVERT: L 60 ARG cc_start: 0.8219 (ptt-90) cc_final: 0.7951 (ptt-90) REVERT: L 103 LEU cc_start: 0.8682 (tp) cc_final: 0.8330 (tt) outliers start: 18 outliers final: 16 residues processed: 96 average time/residue: 0.4898 time to fit residues: 49.7145 Evaluate side-chains 100 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 276 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 362 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 567 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 593 CYS Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 656 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 57 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.102225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.069353 restraints weight = 10750.163| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.27 r_work: 0.2887 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6688 Z= 0.108 Angle : 0.487 7.124 9093 Z= 0.259 Chirality : 0.043 0.143 978 Planarity : 0.004 0.042 1173 Dihedral : 4.424 42.390 915 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.70 % Allowed : 16.79 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: 0.81 (0.29), residues: 804 helix: 2.12 (0.54), residues: 100 sheet: 0.76 (0.30), residues: 283 loop : 0.07 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 24 TYR 0.017 0.001 TYR A 650 PHE 0.016 0.001 PHE A 282 TRP 0.014 0.001 TRP L 90 HIS 0.003 0.001 HIS A 531 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6681) covalent geometry : angle 0.48501 ( 9079) SS BOND : bond 0.00385 ( 7) SS BOND : angle 1.26182 ( 14) hydrogen bonds : bond 0.03199 ( 230) hydrogen bonds : angle 4.76756 ( 747) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5270.98 seconds wall clock time: 90 minutes 8.31 seconds (5408.31 seconds total)