Starting phenix.real_space_refine on Thu Jul 2 14:13:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8g0l_29657/07_2026/8g0l_29657.cif Found real_map, /net/cci-nas-00/data/ceres_data/8g0l_29657/07_2026/8g0l_29657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8g0l_29657/07_2026/8g0l_29657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8g0l_29657/07_2026/8g0l_29657.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8g0l_29657/07_2026/8g0l_29657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8g0l_29657/07_2026/8g0l_29657.map" } resolution = 3.39 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= 0.029 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 P 1 5.49 5 S 48 5.16 5 C 5674 2.51 5 N 1487 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8872 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1274 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 6, 'TRANS': 151} Chain: "B" Number of atoms: 7531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 925, 7531 Classifications: {'peptide': 925} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 891} Chain breaks: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Chain: "C" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'CMC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'CMC:plan-1': 1, 'CMC:plan-3': 1, 'CMC:plan-5': 1} Unresolved non-hydrogen planarities: 14 Time building chain proxies: 1.61, per 1000 atoms: 0.18 Number of scatterers: 8872 At special positions: 0 Unit cell: (77.4, 111.8, 127.28, 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 P 1 15.00 O 1662 8.00 N 1487 7.00 C 5674 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 203.7 milliseconds 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 2 sheets defined 74.8% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 15 through 20 removed outlier: 3.862A pdb=" N ASN A 19 " --> pdb=" O PHE A 15 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 15 through 20' Processing helix chain 'A' and resid 28 through 39 Processing helix chain 'A' and resid 81 through 84 removed outlier: 3.895A pdb=" N ARG A 84 " --> pdb=" O PRO A 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 81 through 84' Processing helix chain 'A' and resid 87 through 103 removed outlier: 3.532A pdb=" N LYS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'B' and resid 10 through 24 Proline residue: B 17 - end of helix Processing helix chain 'B' and resid 26 through 41 removed outlier: 3.860A pdb=" N LYS B 40 " --> pdb=" O LYS B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 58 Processing helix chain 'B' and resid 61 through 74 removed outlier: 3.521A pdb=" N LEU B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.887A pdb=" N MET B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 109 removed outlier: 3.700A pdb=" N THR B 99 " --> pdb=" O PRO B 95 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 100 " --> pdb=" O GLU B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 127 Processing helix chain 'B' and resid 128 through 143 Processing helix chain 'B' and resid 145 through 163 removed outlier: 3.639A pdb=" N TYR B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 172 Processing helix chain 'B' and resid 172 through 188 removed outlier: 3.699A pdb=" N LEU B 176 " --> pdb=" O MET B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 206 Processing helix chain 'B' and resid 208 through 218 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 244 through 259 Processing helix chain 'B' and resid 262 through 280 Processing helix chain 'B' and resid 298 through 316 removed outlier: 3.638A pdb=" N LYS B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER B 316 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 338 removed outlier: 3.739A pdb=" N LEU B 325 " --> pdb=" O ARG B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 359 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.903A pdb=" N VAL B 371 " --> pdb=" O THR B 367 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 376 No H-bonds generated for 'chain 'B' and resid 374 through 376' Processing helix chain 'B' and resid 380 through 389 Processing helix chain 'B' and resid 407 through 424 Processing helix chain 'B' and resid 425 through 429 Processing helix chain 'B' and resid 431 through 450 Processing helix chain 'B' and resid 464 through 483 removed outlier: 3.917A pdb=" N CYS B 468 " --> pdb=" O SER B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 502 removed outlier: 3.933A pdb=" N VAL B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS B 501 " --> pdb=" O GLU B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 520 Processing helix chain 'B' and resid 522 through 533 removed outlier: 3.856A pdb=" N VAL B 526 " --> pdb=" O PHE B 522 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP B 527 " --> pdb=" O GLU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 543 removed outlier: 4.283A pdb=" N ASP B 540 " --> pdb=" O HIS B 536 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR B 541 " --> pdb=" O ILE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 551 removed outlier: 3.893A pdb=" N TYR B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU B 551 " --> pdb=" O THR B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 554 No H-bonds generated for 'chain 'B' and resid 552 through 554' Processing helix chain 'B' and resid 555 through 588 removed outlier: 4.760A pdb=" N SER B 578 " --> pdb=" O GLN B 574 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 591 No H-bonds generated for 'chain 'B' and resid 589 through 591' Processing helix chain 'B' and resid 592 through 605 Processing helix chain 'B' and resid 606 through 624 removed outlier: 3.707A pdb=" N GLU B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 639 Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.868A pdb=" N LEU B 652 " --> pdb=" O TRP B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 699 Processing helix chain 'B' and resid 700 through 704 Processing helix chain 'B' and resid 723 through 746 Processing helix chain 'B' and resid 760 through 768 removed outlier: 3.555A pdb=" N GLY B 768 " --> pdb=" O PHE B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 790 removed outlier: 3.826A pdb=" N CYS B 772 " --> pdb=" O GLY B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 819 removed outlier: 3.546A pdb=" N CYS B 819 " --> pdb=" O VAL B 815 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 870 removed outlier: 4.100A pdb=" N LEU B 838 " --> pdb=" O HIS B 834 " (cutoff:3.500A) Proline residue: B 864 - end of helix Processing helix chain 'B' and resid 885 through 917 Processing helix chain 'B' and resid 932 through 966 removed outlier: 3.758A pdb=" N GLU B 965 " --> pdb=" O LYS B 961 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR B 966 " --> pdb=" O LYS B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 971 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 4.305A pdb=" N GLY A 55 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N MET A 54 " --> pdb=" O VAL A 79 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL A 79 " --> pdb=" O MET A 54 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR A 56 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU A 77 " --> pdb=" O TYR A 56 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N MET A 58 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N PHE A 111 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ALA A 76 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 12.722A pdb=" N ARG A 113 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 14.278A pdb=" N SER A 78 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ARG A 153 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N VAL A 130 " --> pdb=" O ARG A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 825 through 827 589 hydrogen bonds defined for protein. 1710 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: 1.04 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1483 1.31 - 1.44: 2353 1.44 - 1.57: 5135 1.57 - 1.70: 1 1.70 - 1.82: 79 Bond restraints: 9051 Sorted by residual: bond pdb=" C2 CMC C 201 " pdb=" O21 CMC C 201 " ideal model delta sigma weight residual 1.245 1.400 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" O3A CMC C 201 " pdb=" P2A CMC C 201 " ideal model delta sigma weight residual 1.658 1.510 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C9P CMC C 201 " pdb=" N8P CMC C 201 " ideal model delta sigma weight residual 1.341 1.472 -0.131 2.00e-02 2.50e+03 4.27e+01 bond pdb=" C5P CMC C 201 " pdb=" N4P CMC C 201 " ideal model delta sigma weight residual 1.344 1.469 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C5P CMC C 201 " pdb=" O5P CMC C 201 " ideal model delta sigma weight residual 1.224 1.180 0.044 2.00e-02 2.50e+03 4.76e+00 ... (remaining 9046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 12126 2.53 - 5.06: 74 5.06 - 7.59: 6 7.59 - 10.12: 5 10.12 - 12.65: 3 Bond angle restraints: 12214 Sorted by residual: angle pdb=" O4A CMC C 201 " pdb=" P2A CMC C 201 " pdb=" O5A CMC C 201 " ideal model delta sigma weight residual 122.23 109.58 12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" O3A CMC C 201 " pdb=" P2A CMC C 201 " pdb=" O6A CMC C 201 " ideal model delta sigma weight residual 96.94 109.42 -12.48 3.00e+00 1.11e-01 1.73e+01 angle pdb=" CB MET B 121 " pdb=" CG MET B 121 " pdb=" SD MET B 121 " ideal model delta sigma weight residual 112.70 124.14 -11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CA GLN A 125 " pdb=" CB GLN A 125 " pdb=" CG GLN A 125 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB MET A 152 " pdb=" CG MET A 152 " pdb=" SD MET A 152 " ideal model delta sigma weight residual 112.70 121.91 -9.21 3.00e+00 1.11e-01 9.42e+00 ... (remaining 12209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.50: 5277 33.50 - 67.01: 225 67.01 - 100.51: 15 100.51 - 134.01: 0 134.01 - 167.51: 3 Dihedral angle restraints: 5520 sinusoidal: 2312 harmonic: 3208 Sorted by residual: dihedral pdb=" CDP CMC C 201 " pdb=" CBP CMC C 201 " pdb=" CCP CMC C 201 " pdb=" O6A CMC C 201 " ideal model delta sinusoidal sigma weight residual 191.32 23.81 167.51 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CAP CMC C 201 " pdb=" CBP CMC C 201 " pdb=" CCP CMC C 201 " pdb=" O6A CMC C 201 " ideal model delta sinusoidal sigma weight residual 70.77 -96.60 167.37 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CEP CMC C 201 " pdb=" CBP CMC C 201 " pdb=" CCP CMC C 201 " pdb=" O6A CMC C 201 " ideal model delta sinusoidal sigma weight residual 308.64 143.50 165.14 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 5517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 960 0.029 - 0.057: 245 0.057 - 0.086: 97 0.086 - 0.115: 43 0.115 - 0.143: 5 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CB ILE B 582 " pdb=" CA ILE B 582 " pdb=" CG1 ILE B 582 " pdb=" CG2 ILE B 582 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CAP CMC C 201 " pdb=" C9P CMC C 201 " pdb=" CBP CMC C 201 " pdb=" OAP CMC C 201 " both_signs ideal model delta sigma weight residual False -2.38 -2.51 0.13 2.00e-01 2.50e+01 3.98e-01 chirality pdb=" CA PRO B 323 " pdb=" N PRO B 323 " pdb=" C PRO B 323 " pdb=" CB PRO B 323 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.57e-01 ... (remaining 1347 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 21 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 22 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 16 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO B 17 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO B 17 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 17 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 757 " -0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO B 758 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 758 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 758 " -0.015 5.00e-02 4.00e+02 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2489 2.81 - 3.33: 8950 3.33 - 3.86: 14475 3.86 - 4.38: 15347 4.38 - 4.90: 26900 Nonbonded interactions: 68161 Sorted by model distance: nonbonded pdb=" O ASN B 167 " pdb=" OG1 THR B 171 " model vdw 2.289 3.040 nonbonded pdb=" O TYR B 149 " pdb=" OG SER B 152 " model vdw 2.314 3.040 nonbonded pdb=" OE1 GLN B 555 " pdb=" OG SER B 952 " model vdw 2.320 3.040 nonbonded pdb=" OD2 ASP B 484 " pdb=" OG1 THR B 486 " model vdw 2.353 3.040 nonbonded pdb=" N GLN B 61 " pdb=" OE1 GLN B 61 " model vdw 2.358 3.120 ... (remaining 68156 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: 2.730 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.180 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9039 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 : 0.004 0.155 9052 Z= 0.187 Angle : 0.526 12.647 12214 Z= 0.248 Chirality : 0.034 0.143 1350 Planarity : 0.003 0.029 1555 Dihedral : 17.717 167.514 3442 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.10 % Allowed : 23.49 % Favored : 76.41 % 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: 3.32 (0.27), residues: 1074 helix: 3.43 (0.19), residues: 750 sheet: 0.10 (1.45), residues: 16 loop : -1.04 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 723 TYR 0.015 0.001 TYR B 580 PHE 0.010 0.001 PHE B 150 TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 ( 9051) covalent geometry : angle 0.52629 / 0.25 (12214) hydrogen bonds : bond 0.13040 / 8.15 ( 589) hydrogen bonds : angle 4.05705 / 2.78 ( 1710) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.216 Fit side-chains REVERT: B 172 MET cc_start: 0.9113 (mmp) cc_final: 0.8710 (mmp) REVERT: B 340 ASN cc_start: 0.9251 (m-40) cc_final: 0.8864 (p0) outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.0612 time to fit residues: 3.9712 Evaluate side-chains 40 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 419 GLN B 555 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.035800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2509 r_free = 0.2509 target = 0.026371 restraints weight = 55405.558| |-----------------------------------------------------------------------------| r_work (start): 0.2475 rms_B_bonded: 4.62 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.0697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9052 Z= 0.099 Angle : 0.443 6.244 12214 Z= 0.227 Chirality : 0.035 0.164 1350 Planarity : 0.003 0.029 1555 Dihedral : 10.033 163.656 1218 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.44 % Allowed : 21.23 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.34 (0.27), residues: 1074 helix: 3.32 (0.19), residues: 764 sheet: -1.00 (0.82), residues: 38 loop : -0.74 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 333 TYR 0.018 0.001 TYR B 580 PHE 0.030 0.001 PHE C 4 TRP 0.005 0.001 TRP B 281 HIS 0.003 0.001 HIS A 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 ( 9051) covalent geometry : angle 0.44346 / 0.23 (12214) hydrogen bonds : bond 0.03733 / 2.43 ( 589) hydrogen bonds : angle 3.29812 / 2.25 ( 1710) Misc. bond : bond 0.00093 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.234 Fit side-chains REVERT: A 152 MET cc_start: 0.8786 (mmm) cc_final: 0.8508 (mmm) REVERT: B 172 MET cc_start: 0.9224 (mmp) cc_final: 0.8810 (mmp) REVERT: B 340 ASN cc_start: 0.9455 (m-40) cc_final: 0.9105 (p0) REVERT: B 641 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8583 (ttm-80) REVERT: C 5 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.9185 (mmm) outliers start: 14 outliers final: 3 residues processed: 52 average time/residue: 0.0692 time to fit residues: 5.4279 Evaluate side-chains 42 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain C residue 5 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.3980 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.025488 restraints weight = 56121.106| |-----------------------------------------------------------------------------| r_work (start): 0.2503 rms_B_bonded: 4.72 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9052 Z= 0.108 Angle : 0.435 8.165 12214 Z= 0.220 Chirality : 0.034 0.130 1350 Planarity : 0.003 0.032 1555 Dihedral : 9.510 161.318 1218 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.13 % Allowed : 21.23 % Favored : 77.64 % 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: 3.37 (0.27), residues: 1074 helix: 3.36 (0.19), residues: 763 sheet: -1.10 (0.92), residues: 30 loop : -0.78 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 318 TYR 0.017 0.001 TYR B 580 PHE 0.011 0.001 PHE B 150 TRP 0.005 0.001 TRP B 281 HIS 0.002 0.000 HIS B 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 9051) covalent geometry : angle 0.43502 / 0.22 (12214) hydrogen bonds : bond 0.03705 / 2.42 ( 589) hydrogen bonds : angle 3.26171 / 2.25 ( 1710) Misc. bond : bond 0.00028 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.251 Fit side-chains REVERT: A 151 ASP cc_start: 0.8936 (t0) cc_final: 0.8588 (t0) REVERT: A 152 MET cc_start: 0.8817 (mmm) cc_final: 0.8512 (mmm) REVERT: B 340 ASN cc_start: 0.9489 (m-40) cc_final: 0.9160 (p0) REVERT: B 641 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8607 (ttm-80) outliers start: 11 outliers final: 3 residues processed: 49 average time/residue: 0.0507 time to fit residues: 3.9730 Evaluate side-chains 43 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 641 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 14 optimal weight: 6.9990 chunk 48 optimal weight: 0.0020 chunk 37 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.036727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.026580 restraints weight = 59225.575| |-----------------------------------------------------------------------------| r_work (start): 0.2475 rms_B_bonded: 4.79 r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9116 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9052 Z= 0.127 Angle : 0.449 7.413 12214 Z= 0.226 Chirality : 0.035 0.126 1350 Planarity : 0.003 0.032 1555 Dihedral : 9.365 160.297 1215 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.23 % Allowed : 22.26 % Favored : 76.51 % 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: 3.38 (0.27), residues: 1074 helix: 3.38 (0.19), residues: 762 sheet: -1.04 (0.90), residues: 30 loop : -0.80 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 318 TYR 0.017 0.001 TYR B 580 PHE 0.012 0.001 PHE B 150 TRP 0.004 0.001 TRP B 281 HIS 0.002 0.001 HIS B 834 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9051) covalent geometry : angle 0.44887 / 0.23 (12214) hydrogen bonds : bond 0.03783 / 2.49 ( 589) hydrogen bonds : angle 3.31271 / 2.29 ( 1710) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.353 Fit side-chains REVERT: A 152 MET cc_start: 0.8910 (mmm) cc_final: 0.8360 (mmm) REVERT: B 29 MET cc_start: 0.9806 (mpp) cc_final: 0.9423 (ptp) REVERT: B 340 ASN cc_start: 0.9459 (m-40) cc_final: 0.9151 (p0) REVERT: B 641 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8672 (ttm-80) outliers start: 12 outliers final: 6 residues processed: 49 average time/residue: 0.0697 time to fit residues: 5.1247 Evaluate side-chains 46 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain C residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 73 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.4980 chunk 23 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.035100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.025354 restraints weight = 56301.095| |-----------------------------------------------------------------------------| r_work (start): 0.2497 rms_B_bonded: 4.74 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9052 Z= 0.103 Angle : 0.437 6.560 12214 Z= 0.221 Chirality : 0.034 0.125 1350 Planarity : 0.003 0.032 1555 Dihedral : 9.324 159.965 1215 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.54 % Allowed : 21.95 % Favored : 76.51 % 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: 3.38 (0.27), residues: 1074 helix: 3.35 (0.19), residues: 762 sheet: -0.82 (0.89), residues: 30 loop : -0.75 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 318 TYR 0.016 0.001 TYR B 580 PHE 0.012 0.001 PHE B 150 TRP 0.005 0.001 TRP B 281 HIS 0.002 0.000 HIS B 428 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 ( 9051) covalent geometry : angle 0.43716 / 0.22 (12214) hydrogen bonds : bond 0.03558 / 2.34 ( 589) hydrogen bonds : angle 3.21006 / 2.22 ( 1710) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.336 Fit side-chains REVERT: A 152 MET cc_start: 0.8876 (mmm) cc_final: 0.8241 (mmm) REVERT: B 29 MET cc_start: 0.9798 (mpp) cc_final: 0.9459 (ptp) REVERT: B 172 MET cc_start: 0.8983 (mmp) cc_final: 0.8669 (mmp) REVERT: B 340 ASN cc_start: 0.9508 (m-40) cc_final: 0.9224 (p0) outliers start: 15 outliers final: 10 residues processed: 53 average time/residue: 0.0716 time to fit residues: 5.8339 Evaluate side-chains 49 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 760 ARG Chi-restraints excluded: chain C residue 1 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 33 GLN B 229 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.034051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2393 r_free = 0.2393 target = 0.024290 restraints weight = 57099.847| |-----------------------------------------------------------------------------| r_work (start): 0.2420 rms_B_bonded: 4.72 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9100 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9052 Z= 0.175 Angle : 0.497 7.113 12214 Z= 0.250 Chirality : 0.035 0.129 1350 Planarity : 0.003 0.032 1555 Dihedral : 9.357 160.188 1215 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.64 % Allowed : 21.74 % Favored : 76.62 % 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: 3.45 (0.27), residues: 1074 helix: 3.42 (0.19), residues: 757 sheet: -0.90 (0.89), residues: 30 loop : -0.67 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 760 TYR 0.016 0.001 TYR B 580 PHE 0.013 0.001 PHE B 150 TRP 0.006 0.001 TRP B 853 HIS 0.002 0.001 HIS B 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 ( 9051) covalent geometry : angle 0.49685 / 0.25 (12214) hydrogen bonds : bond 0.04234 / 2.79 ( 589) hydrogen bonds : angle 3.47489 / 2.42 ( 1710) Misc. bond : bond 0.00033 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 39 time to evaluate : 0.362 Fit side-chains REVERT: A 151 ASP cc_start: 0.8752 (t0) cc_final: 0.8546 (t0) REVERT: A 152 MET cc_start: 0.8896 (mmm) cc_final: 0.8171 (mmm) REVERT: B 340 ASN cc_start: 0.9516 (m-40) cc_final: 0.9232 (p0) REVERT: B 641 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8646 (ttm-80) outliers start: 16 outliers final: 9 residues processed: 53 average time/residue: 0.0713 time to fit residues: 5.7600 Evaluate side-chains 48 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 15 PHE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 760 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 0.0050 chunk 42 optimal weight: 0.0030 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.035609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.025764 restraints weight = 55895.383| |-----------------------------------------------------------------------------| r_work (start): 0.2436 rms_B_bonded: 4.85 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9052 Z= 0.090 Angle : 0.453 8.245 12214 Z= 0.225 Chirality : 0.034 0.127 1350 Planarity : 0.003 0.033 1555 Dihedral : 9.315 159.916 1215 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.23 % Allowed : 22.36 % Favored : 76.41 % 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: 3.38 (0.27), residues: 1074 helix: 3.35 (0.19), residues: 760 sheet: -0.45 (0.90), residues: 30 loop : -0.78 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 445 TYR 0.017 0.001 TYR B 580 PHE 0.012 0.001 PHE B 150 TRP 0.008 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00187 / 0.09 ( 9051) covalent geometry : angle 0.45326 / 0.23 (12214) hydrogen bonds : bond 0.03241 / 2.14 ( 589) hydrogen bonds : angle 3.12360 / 2.15 ( 1710) Misc. bond : bond 0.00029 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.347 Fit side-chains REVERT: A 151 ASP cc_start: 0.8681 (t0) cc_final: 0.8480 (t0) REVERT: A 152 MET cc_start: 0.8897 (mmm) cc_final: 0.8193 (mmm) REVERT: B 29 MET cc_start: 0.9787 (mpp) cc_final: 0.9419 (ptp) REVERT: B 172 MET cc_start: 0.9537 (tpp) cc_final: 0.9296 (mmp) REVERT: B 340 ASN cc_start: 0.9555 (m-40) cc_final: 0.9278 (p0) REVERT: B 641 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8766 (ttm110) outliers start: 12 outliers final: 7 residues processed: 53 average time/residue: 0.0702 time to fit residues: 5.7639 Evaluate side-chains 50 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 536 HIS Chi-restraints excluded: chain B residue 587 TYR Chi-restraints excluded: chain B residue 641 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 81 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 229 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.035178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.025406 restraints weight = 56877.201| |-----------------------------------------------------------------------------| r_work (start): 0.2468 rms_B_bonded: 4.76 r_work (final): 0.2468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9052 Z= 0.114 Angle : 0.470 8.476 12214 Z= 0.231 Chirality : 0.036 0.328 1350 Planarity : 0.003 0.032 1555 Dihedral : 9.329 159.547 1215 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.92 % Allowed : 22.56 % Favored : 76.51 % 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: 3.41 (0.27), residues: 1074 helix: 3.37 (0.19), residues: 761 sheet: -0.48 (0.91), residues: 30 loop : -0.74 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 613 TYR 0.017 0.001 TYR B 580 PHE 0.024 0.001 PHE C 4 TRP 0.004 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 ( 9051) covalent geometry : angle 0.47013 / 0.23 (12214) hydrogen bonds : bond 0.03465 / 2.28 ( 589) hydrogen bonds : angle 3.23452 / 2.24 ( 1710) Misc. bond : bond 0.00021 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.371 Fit side-chains REVERT: A 152 MET cc_start: 0.8991 (mmm) cc_final: 0.8229 (mmm) REVERT: B 29 MET cc_start: 0.9779 (mpp) cc_final: 0.9398 (ptp) REVERT: B 340 ASN cc_start: 0.9502 (m-40) cc_final: 0.9251 (p0) outliers start: 9 outliers final: 7 residues processed: 49 average time/residue: 0.0773 time to fit residues: 6.0289 Evaluate side-chains 48 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 464 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 99 optimal weight: 0.3980 chunk 11 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 414 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.035552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.025758 restraints weight = 55446.519| |-----------------------------------------------------------------------------| r_work (start): 0.2436 rms_B_bonded: 4.82 r_work (final): 0.2436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9052 Z= 0.092 Angle : 0.470 10.440 12214 Z= 0.229 Chirality : 0.035 0.242 1350 Planarity : 0.003 0.033 1555 Dihedral : 9.278 159.311 1215 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.13 % Allowed : 22.67 % Favored : 76.21 % 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: 3.39 (0.27), residues: 1074 helix: 3.33 (0.19), residues: 760 sheet: -0.28 (0.94), residues: 30 loop : -0.69 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 641 TYR 0.017 0.001 TYR B 580 PHE 0.011 0.001 PHE B 150 TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 ( 9051) covalent geometry : angle 0.46991 / 0.23 (12214) hydrogen bonds : bond 0.03223 / 2.12 ( 589) hydrogen bonds : angle 3.13709 / 2.17 ( 1710) Misc. bond : bond 0.00101 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.355 Fit side-chains REVERT: A 152 MET cc_start: 0.8933 (mmm) cc_final: 0.8154 (mmm) REVERT: B 29 MET cc_start: 0.9794 (mpp) cc_final: 0.9407 (ptp) REVERT: B 340 ASN cc_start: 0.9511 (m-40) cc_final: 0.9278 (p0) outliers start: 11 outliers final: 8 residues processed: 50 average time/residue: 0.0786 time to fit residues: 6.1854 Evaluate side-chains 49 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 587 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 46 optimal weight: 0.0060 chunk 37 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 79 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.035921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.026104 restraints weight = 55424.811| |-----------------------------------------------------------------------------| r_work (start): 0.2448 rms_B_bonded: 4.88 r_work (final): 0.2448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9052 Z= 0.090 Angle : 0.500 11.832 12214 Z= 0.239 Chirality : 0.035 0.239 1350 Planarity : 0.003 0.033 1555 Dihedral : 9.274 158.651 1215 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.72 % Allowed : 23.18 % Favored : 76.10 % 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: 3.41 (0.27), residues: 1074 helix: 3.33 (0.19), residues: 760 sheet: -0.08 (0.96), residues: 30 loop : -0.66 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 641 TYR 0.017 0.001 TYR B 580 PHE 0.023 0.001 PHE C 4 TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00194 / 0.09 ( 9051) covalent geometry : angle 0.50037 / 0.24 (12214) hydrogen bonds : bond 0.03066 / 2.02 ( 589) hydrogen bonds : angle 3.08973 / 2.13 ( 1710) Misc. bond : bond 0.00002 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2148 Ramachandran restraints generated. 1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.387 Fit side-chains REVERT: A 152 MET cc_start: 0.8915 (mmm) cc_final: 0.8126 (mmm) REVERT: B 29 MET cc_start: 0.9790 (mpp) cc_final: 0.9407 (ptp) REVERT: B 340 ASN cc_start: 0.9498 (m-40) cc_final: 0.9273 (p0) outliers start: 7 outliers final: 7 residues processed: 47 average time/residue: 0.0728 time to fit residues: 5.6730 Evaluate side-chains 48 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain B residue 167 ASN Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 587 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 67 optimal weight: 5.9990 chunk 94 optimal weight: 0.0470 chunk 93 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 35 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.036144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.026407 restraints weight = 55054.336| |-----------------------------------------------------------------------------| r_work (start): 0.2458 rms_B_bonded: 4.84 r_work (final): 0.2458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9052 Z= 0.088 Angle : 0.495 11.865 12214 Z= 0.235 Chirality : 0.035 0.230 1350 Planarity : 0.003 0.033 1555 Dihedral : 9.202 158.307 1215 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.72 % Allowed : 22.97 % Favored : 76.31 % 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: 3.41 (0.27), residues: 1074 helix: 3.32 (0.19), residues: 760 sheet: 0.08 (0.97), residues: 30 loop : -0.63 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 641 TYR 0.017 0.001 TYR B 580 PHE 0.010 0.001 PHE B 150 TRP 0.006 0.001 TRP B 281 HIS 0.002 0.000 HIS B 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 ( 9051) covalent geometry : angle 0.49469 / 0.24 (12214) hydrogen bonds : bond 0.02973 / 1.95 ( 589) hydrogen bonds : angle 3.06532 / 2.11 ( 1710) Misc. bond : bond 0.00031 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1273.41 seconds wall clock time: 22 minutes 46.19 seconds (1366.19 seconds total)