Starting phenix.real_space_refine on Thu Jul 2 02:20:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gni_34165/07_2026/8gni_34165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gni_34165/07_2026/8gni_34165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gni_34165/07_2026/8gni_34165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gni_34165/07_2026/8gni_34165.map" model { file = "/net/cci-nas-00/data/ceres_data/8gni_34165/07_2026/8gni_34165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gni_34165/07_2026/8gni_34165.cif" } resolution = 3.74 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= 0.015 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 28 5.16 5 C 3670 2.51 5 N 1042 2.21 5 O 1091 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5832 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3821 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 16, 'TRANS': 475} Chain: "B" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1125 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "C" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 864 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.30, per 1000 atoms: 0.22 Number of scatterers: 5832 At special positions: 0 Unit cell: (86.08, 100.068, 119.436, 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 28 16.00 P 1 15.00 O 1091 8.00 N 1042 7.00 C 3670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.46 Conformation dependent library (CDL) restraints added in 207.9 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1384 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 4 sheets defined 58.6% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 58 through 81 removed outlier: 3.695A pdb=" N ASP A 63 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ARG A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 83 through 98 removed outlier: 3.727A pdb=" N ALA A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ALA A 90 " --> pdb=" O ARG A 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 Processing helix chain 'A' and resid 110 through 122 removed outlier: 4.849A pdb=" N ASP A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ALA A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.878A pdb=" N GLN A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 removed outlier: 4.049A pdb=" N LEU A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 removed outlier: 3.976A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 172 Processing helix chain 'A' and resid 177 through 193 removed outlier: 3.809A pdb=" N SER A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.788A pdb=" N ALA A 210 " --> pdb=" O GLY A 206 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 211 " --> pdb=" O GLY A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 219 through 231 removed outlier: 3.720A pdb=" N GLY A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 246 removed outlier: 3.910A pdb=" N VAL A 246 " --> pdb=" O GLN A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 259 Processing helix chain 'A' and resid 263 through 276 removed outlier: 3.655A pdb=" N ARG A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 4.304A pdb=" N ARG A 285 " --> pdb=" O LYS A 281 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.518A pdb=" N LEU A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 326 through 329 removed outlier: 3.516A pdb=" N ARG A 329 " --> pdb=" O ASP A 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 326 through 329' Processing helix chain 'A' and resid 330 through 335 removed outlier: 3.803A pdb=" N LEU A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 330 through 335' Processing helix chain 'A' and resid 338 through 358 removed outlier: 4.176A pdb=" N LEU A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 removed outlier: 4.416A pdb=" N THR A 362 " --> pdb=" O GLN A 359 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N LYS A 363 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 364 " --> pdb=" O LYS A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 376 removed outlier: 3.674A pdb=" N SER A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 398 Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 429 through 436 Processing helix chain 'A' and resid 439 through 445 removed outlier: 3.711A pdb=" N ARG A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 Processing helix chain 'A' and resid 459 through 476 removed outlier: 3.535A pdb=" N ARG A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE A 476 " --> pdb=" O GLU A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 495 removed outlier: 3.991A pdb=" N TRP A 490 " --> pdb=" O ASN A 486 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 removed outlier: 4.398A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.573A pdb=" N VAL A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 519 through 526 Processing helix chain 'A' and resid 531 through 543 Processing helix chain 'B' and resid 574 through 587 Processing helix chain 'B' and resid 599 through 604 removed outlier: 3.502A pdb=" N LYS B 602 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE B 603 " --> pdb=" O ALA B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.855A pdb=" N LYS B 628 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 650 removed outlier: 4.245A pdb=" N ALA B 646 " --> pdb=" O GLU B 642 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 removed outlier: 3.518A pdb=" N THR B 677 " --> pdb=" O ALA B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 691 through 696 Processing sheet with id=AA1, first strand: chain 'B' and resid 591 through 593 removed outlier: 6.777A pdb=" N VAL B 564 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N PHE B 565 " --> pdb=" O VAL B 618 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N VAL B 620 " --> pdb=" O PHE B 565 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N SER B 567 " --> pdb=" O VAL B 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 5 through 8 Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 13 removed outlier: 6.826A pdb=" N MET C 35 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL C 51 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP C 37 " --> pdb=" O VAL C 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 13 267 hydrogen bonds defined for protein. 738 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: 0.68 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1949 1.34 - 1.46: 1020 1.46 - 1.58: 2922 1.58 - 1.70: 1 1.70 - 1.81: 38 Bond restraints: 5930 Sorted by residual: bond pdb=" O5R NMN A1001 " pdb=" P NMN A1001 " ideal model delta sigma weight residual 1.730 1.614 0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C5R NMN A1001 " pdb=" O5R NMN A1001 " ideal model delta sigma weight residual 1.389 1.448 -0.059 2.00e-02 2.50e+03 8.58e+00 bond pdb=" C SER B 622 " pdb=" N PRO B 623 " ideal model delta sigma weight residual 1.334 1.401 -0.068 2.34e-02 1.83e+03 8.34e+00 bond pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta sigma weight residual 1.454 1.494 -0.040 1.50e-02 4.44e+03 7.16e+00 bond pdb=" C1R NMN A1001 " pdb=" O4R NMN A1001 " ideal model delta sigma weight residual 1.370 1.421 -0.051 2.00e-02 2.50e+03 6.62e+00 ... (remaining 5925 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 7835 2.94 - 5.89: 161 5.89 - 8.83: 23 8.83 - 11.78: 6 11.78 - 14.72: 1 Bond angle restraints: 8026 Sorted by residual: angle pdb=" N ALA A 102 " pdb=" CA ALA A 102 " pdb=" C ALA A 102 " ideal model delta sigma weight residual 113.18 107.98 5.20 1.21e+00 6.83e-01 1.85e+01 angle pdb=" CA LEU A 327 " pdb=" CB LEU A 327 " pdb=" CG LEU A 327 " ideal model delta sigma weight residual 116.30 131.02 -14.72 3.50e+00 8.16e-02 1.77e+01 angle pdb=" CA LYS A 80 " pdb=" CB LYS A 80 " pdb=" CG LYS A 80 " ideal model delta sigma weight residual 114.10 122.12 -8.02 2.00e+00 2.50e-01 1.61e+01 angle pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 112.89 107.93 4.96 1.24e+00 6.50e-01 1.60e+01 angle pdb=" N ARG A 110 " pdb=" CA ARG A 110 " pdb=" C ARG A 110 " ideal model delta sigma weight residual 111.56 105.58 5.98 1.53e+00 4.27e-01 1.53e+01 ... (remaining 8021 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3244 17.82 - 35.63: 319 35.63 - 53.45: 43 53.45 - 71.26: 11 71.26 - 89.08: 6 Dihedral angle restraints: 3623 sinusoidal: 1480 harmonic: 2143 Sorted by residual: dihedral pdb=" CA ALA A 107 " pdb=" C ALA A 107 " pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta harmonic sigma weight residual 180.00 158.31 21.69 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA PRO B 623 " pdb=" C PRO B 623 " pdb=" N GLY B 624 " pdb=" CA GLY B 624 " ideal model delta harmonic sigma weight residual 180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 96 " pdb=" CB CYS C 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.50 33.50 1 1.00e+01 1.00e-02 1.60e+01 ... (remaining 3620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 703 0.059 - 0.117: 173 0.117 - 0.176: 28 0.176 - 0.235: 9 0.235 - 0.293: 3 Chirality restraints: 916 Sorted by residual: chirality pdb=" CB VAL A 506 " pdb=" CA VAL A 506 " pdb=" CG1 VAL A 506 " pdb=" CG2 VAL A 506 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB ILE A 120 " pdb=" CA ILE A 120 " pdb=" CG1 ILE A 120 " pdb=" CG2 ILE A 120 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 913 not shown) Planarity restraints: 1040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 107 " 0.019 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C ALA A 107 " -0.069 2.00e-02 2.50e+03 pdb=" O ALA A 107 " 0.026 2.00e-02 2.50e+03 pdb=" N VAL A 108 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 654 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.82e+00 pdb=" N PRO B 655 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 655 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 655 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 100 " 0.016 2.00e-02 2.50e+03 3.12e-02 9.72e+00 pdb=" C VAL C 100 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL C 100 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU C 101 " 0.018 2.00e-02 2.50e+03 ... (remaining 1037 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 54 2.56 - 3.15: 4526 3.15 - 3.73: 8985 3.73 - 4.32: 12208 4.32 - 4.90: 19936 Nonbonded interactions: 45709 Sorted by model distance: nonbonded pdb=" OE2 GLU A 264 " pdb=" CD2 LEU A 303 " model vdw 1.977 3.460 nonbonded pdb=" O LYS A 363 " pdb=" OG SER A 366 " model vdw 2.256 3.040 nonbonded pdb=" O SER A 485 " pdb=" OG SER A 485 " model vdw 2.320 3.040 nonbonded pdb=" O SER A 408 " pdb=" OG SER A 408 " model vdw 2.324 3.040 nonbonded pdb=" ND2 ASN B 652 " pdb=" O LEU B 699 " model vdw 2.326 3.120 ... (remaining 45704 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.330 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 0.005 0.116 5931 Z= 0.253 Angle : 1.040 14.721 8028 Z= 0.564 Chirality : 0.057 0.293 916 Planarity : 0.007 0.078 1040 Dihedral : 14.200 89.075 2236 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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: 740 helix: -2.32 (0.22), residues: 370 sheet: -1.49 (0.55), residues: 64 loop : -2.00 (0.33), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 289 TYR 0.018 0.002 TYR B 687 PHE 0.020 0.002 PHE A 308 TRP 0.020 0.002 TRP C 103 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.25 ( 5930) covalent geometry : angle 1.04005 / 0.56 ( 8026) SS BOND : bond 0.00530 / 0.33 ( 1) SS BOND : angle 0.34187 / 0.14 ( 2) hydrogen bonds : bond 0.14706 / 9.71 ( 260) hydrogen bonds : angle 6.04619 / 4.15 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 ARG cc_start: 0.7620 (mmm160) cc_final: 0.7410 (mmt180) REVERT: A 391 LYS cc_start: 0.8715 (mtmm) cc_final: 0.8409 (mtpp) REVERT: A 436 GLN cc_start: 0.8888 (mm110) cc_final: 0.8575 (mm-40) REVERT: A 464 LYS cc_start: 0.8803 (mttt) cc_final: 0.8538 (mtpt) REVERT: A 547 HIS cc_start: 0.6445 (t70) cc_final: 0.6238 (t70) REVERT: C 77 ASN cc_start: 0.8500 (m-40) cc_final: 0.8237 (m-40) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.0929 time to fit residues: 23.1614 Evaluate side-chains 160 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 190 HIS A 418 GLN B 685 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.165859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.133821 restraints weight = 10618.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.136518 restraints weight = 17029.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137524 restraints weight = 8118.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.137544 restraints weight = 5695.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138146 restraints weight = 5358.410| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5931 Z= 0.185 Angle : 0.712 9.968 8028 Z= 0.350 Chirality : 0.044 0.196 916 Planarity : 0.005 0.058 1040 Dihedral : 5.011 26.259 844 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.77 % Allowed : 13.69 % Favored : 84.54 % 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: -2.00 (0.30), residues: 740 helix: -1.26 (0.25), residues: 381 sheet: -1.12 (0.54), residues: 63 loop : -1.23 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 201 TYR 0.010 0.002 TYR C 60 PHE 0.014 0.002 PHE A 308 TRP 0.009 0.001 TRP A 214 HIS 0.003 0.001 HIS B 633 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.18 ( 5930) covalent geometry : angle 0.71150 / 0.35 ( 8026) SS BOND : bond 0.00952 / 0.59 ( 1) SS BOND : angle 1.79695 / 0.71 ( 2) hydrogen bonds : bond 0.04654 / 3.11 ( 260) hydrogen bonds : angle 4.40421 / 3.13 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.6991 (ptp-170) cc_final: 0.6692 (mpp80) REVERT: A 191 MET cc_start: 0.7358 (tpp) cc_final: 0.7097 (tpt) REVERT: A 267 ARG cc_start: 0.8408 (mtm-85) cc_final: 0.7093 (mtm-85) REVERT: A 338 ARG cc_start: 0.7852 (mmm160) cc_final: 0.7634 (mmt180) REVERT: A 436 GLN cc_start: 0.8858 (mm110) cc_final: 0.8620 (mm-40) REVERT: A 464 LYS cc_start: 0.8800 (mttt) cc_final: 0.8528 (mtpt) REVERT: C 65 LYS cc_start: 0.8674 (ttmm) cc_final: 0.8281 (ttmm) outliers start: 11 outliers final: 10 residues processed: 167 average time/residue: 0.0939 time to fit residues: 19.5361 Evaluate side-chains 159 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 68 optimal weight: 0.3980 chunk 20 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.165831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.121974 restraints weight = 10391.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.124435 restraints weight = 6317.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.126085 restraints weight = 4449.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.127130 restraints weight = 3446.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.127826 restraints weight = 2887.118| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5931 Z= 0.143 Angle : 0.647 8.814 8028 Z= 0.316 Chirality : 0.042 0.146 916 Planarity : 0.004 0.053 1040 Dihedral : 4.812 26.586 844 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.58 % Allowed : 15.94 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.31), residues: 740 helix: -0.59 (0.27), residues: 373 sheet: -1.02 (0.54), residues: 63 loop : -1.03 (0.39), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 543 TYR 0.011 0.001 TYR A 503 PHE 0.021 0.002 PHE A 308 TRP 0.010 0.001 TRP A 103 HIS 0.002 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 5930) covalent geometry : angle 0.64688 / 0.32 ( 8026) SS BOND : bond 0.00746 / 0.47 ( 1) SS BOND : angle 1.86882 / 0.75 ( 2) hydrogen bonds : bond 0.03913 / 2.67 ( 260) hydrogen bonds : angle 4.17117 / 3.01 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.7846 (tpp) cc_final: 0.7500 (tpp) REVERT: A 264 GLU cc_start: 0.7227 (mp0) cc_final: 0.6504 (mp0) REVERT: A 267 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.7005 (mtm-85) REVERT: A 338 ARG cc_start: 0.7889 (mmm160) cc_final: 0.7605 (mmt180) REVERT: A 436 GLN cc_start: 0.8843 (mm110) cc_final: 0.8638 (mm-40) REVERT: A 451 LEU cc_start: 0.9229 (tp) cc_final: 0.9017 (tp) REVERT: B 699 LEU cc_start: 0.7244 (mt) cc_final: 0.6513 (pp) REVERT: C 65 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8344 (ttmm) outliers start: 16 outliers final: 13 residues processed: 164 average time/residue: 0.1064 time to fit residues: 21.6038 Evaluate side-chains 162 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 27 optimal weight: 0.0170 chunk 68 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 57 optimal weight: 0.5980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.165454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.121126 restraints weight = 10570.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123484 restraints weight = 6504.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.125078 restraints weight = 4561.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126086 restraints weight = 3554.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126851 restraints weight = 2980.214| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5931 Z= 0.140 Angle : 0.640 9.162 8028 Z= 0.308 Chirality : 0.041 0.151 916 Planarity : 0.004 0.047 1040 Dihedral : 4.648 25.747 844 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.90 % Allowed : 18.04 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.31), residues: 740 helix: -0.20 (0.27), residues: 368 sheet: -0.73 (0.55), residues: 63 loop : -0.98 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 543 TYR 0.011 0.001 TYR A 503 PHE 0.028 0.002 PHE A 308 TRP 0.012 0.001 TRP A 103 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 5930) covalent geometry : angle 0.63924 / 0.31 ( 8026) SS BOND : bond 0.00462 / 0.29 ( 1) SS BOND : angle 1.37628 / 0.56 ( 2) hydrogen bonds : bond 0.03600 / 2.47 ( 260) hydrogen bonds : angle 4.05033 / 2.95 ( 738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7148 (ptp-170) cc_final: 0.6814 (mpp80) REVERT: A 191 MET cc_start: 0.7980 (tpp) cc_final: 0.7612 (tpp) REVERT: A 264 GLU cc_start: 0.7290 (mp0) cc_final: 0.6829 (mp0) REVERT: A 267 ARG cc_start: 0.8393 (mtm-85) cc_final: 0.7377 (mtm-85) REVERT: B 651 LYS cc_start: 0.4951 (pttm) cc_final: 0.4548 (mtmm) REVERT: B 699 LEU cc_start: 0.7339 (mt) cc_final: 0.6667 (pp) REVERT: C 65 LYS cc_start: 0.8753 (ttmm) cc_final: 0.8339 (ttmm) outliers start: 18 outliers final: 14 residues processed: 161 average time/residue: 0.0969 time to fit residues: 19.5214 Evaluate side-chains 159 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 71 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.165628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.133612 restraints weight = 10644.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135777 restraints weight = 15605.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.136092 restraints weight = 10261.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138326 restraints weight = 6130.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138018 restraints weight = 4462.406| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5931 Z= 0.146 Angle : 0.655 10.427 8028 Z= 0.312 Chirality : 0.042 0.157 916 Planarity : 0.004 0.045 1040 Dihedral : 4.612 25.179 844 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.22 % Allowed : 19.65 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.31), residues: 740 helix: -0.11 (0.27), residues: 368 sheet: -0.71 (0.56), residues: 63 loop : -0.97 (0.38), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 543 TYR 0.009 0.001 TYR C 60 PHE 0.038 0.002 PHE A 308 TRP 0.014 0.001 TRP A 103 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.15 ( 5930) covalent geometry : angle 0.65461 / 0.31 ( 8026) SS BOND : bond 0.00493 / 0.31 ( 1) SS BOND : angle 1.25301 / 0.51 ( 2) hydrogen bonds : bond 0.03586 / 2.46 ( 260) hydrogen bonds : angle 4.03004 / 2.95 ( 738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.7709 (tpp) cc_final: 0.7447 (tpp) REVERT: A 232 ASN cc_start: 0.8270 (m-40) cc_final: 0.7169 (m-40) REVERT: A 310 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.6444 (tpp80) REVERT: B 699 LEU cc_start: 0.7258 (mt) cc_final: 0.6639 (pp) REVERT: C 65 LYS cc_start: 0.8669 (ttmm) cc_final: 0.8269 (ttmm) outliers start: 20 outliers final: 17 residues processed: 155 average time/residue: 0.0942 time to fit residues: 18.2881 Evaluate side-chains 160 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 11 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 28 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.166009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.122525 restraints weight = 10532.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.124918 restraints weight = 6369.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126497 restraints weight = 4468.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.127509 restraints weight = 3468.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128186 restraints weight = 2916.225| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5931 Z= 0.138 Angle : 0.654 9.960 8028 Z= 0.313 Chirality : 0.042 0.158 916 Planarity : 0.004 0.044 1040 Dihedral : 4.748 33.089 844 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.22 % Allowed : 21.10 % Favored : 75.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.79 (0.31), residues: 740 helix: -0.05 (0.27), residues: 370 sheet: -0.73 (0.57), residues: 65 loop : -0.93 (0.38), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 86 TYR 0.009 0.001 TYR A 503 PHE 0.040 0.002 PHE A 308 TRP 0.023 0.002 TRP A 103 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 5930) covalent geometry : angle 0.65392 / 0.31 ( 8026) SS BOND : bond 0.00443 / 0.28 ( 1) SS BOND : angle 1.03114 / 0.42 ( 2) hydrogen bonds : bond 0.03486 / 2.39 ( 260) hydrogen bonds : angle 4.06816 / 2.98 ( 738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 80 LYS cc_start: 0.8405 (pttp) cc_final: 0.8082 (pttt) REVERT: A 191 MET cc_start: 0.8027 (tpp) cc_final: 0.7631 (tpp) REVERT: A 232 ASN cc_start: 0.8185 (m-40) cc_final: 0.7465 (t0) REVERT: A 264 GLU cc_start: 0.7724 (pm20) cc_final: 0.7406 (pm20) REVERT: A 267 ARG cc_start: 0.8184 (mtm-85) cc_final: 0.6935 (mtm-85) REVERT: A 310 ARG cc_start: 0.7501 (mmm-85) cc_final: 0.6643 (tpp80) REVERT: B 678 PHE cc_start: 0.6684 (t80) cc_final: 0.6466 (t80) outliers start: 20 outliers final: 17 residues processed: 154 average time/residue: 0.0924 time to fit residues: 17.8573 Evaluate side-chains 161 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 36 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.164648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.132938 restraints weight = 10572.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133601 restraints weight = 15095.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.133805 restraints weight = 12163.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134427 restraints weight = 7119.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.135413 restraints weight = 5798.862| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5931 Z= 0.155 Angle : 0.677 11.276 8028 Z= 0.324 Chirality : 0.042 0.143 916 Planarity : 0.004 0.041 1040 Dihedral : 4.975 41.053 844 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.38 % Allowed : 22.54 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.31), residues: 740 helix: 0.03 (0.27), residues: 369 sheet: -0.70 (0.58), residues: 65 loop : -0.87 (0.38), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 86 TYR 0.009 0.001 TYR C 60 PHE 0.043 0.002 PHE A 308 TRP 0.034 0.002 TRP A 103 HIS 0.006 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 5930) covalent geometry : angle 0.67718 / 0.32 ( 8026) SS BOND : bond 0.00526 / 0.33 ( 1) SS BOND : angle 1.18359 / 0.48 ( 2) hydrogen bonds : bond 0.03619 / 2.49 ( 260) hydrogen bonds : angle 4.08775 / 3.00 ( 738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.188 Fit side-chains REVERT: A 191 MET cc_start: 0.7774 (tpp) cc_final: 0.7493 (tpp) REVERT: A 232 ASN cc_start: 0.8148 (m-40) cc_final: 0.7849 (t0) REVERT: A 310 ARG cc_start: 0.7246 (mmm-85) cc_final: 0.6483 (tpp80) REVERT: B 699 LEU cc_start: 0.6902 (mt) cc_final: 0.6182 (pp) outliers start: 21 outliers final: 16 residues processed: 151 average time/residue: 0.0989 time to fit residues: 18.6225 Evaluate side-chains 157 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 564 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 40 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 55 optimal weight: 0.4980 chunk 36 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 overall best weight: 0.3338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS A 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.123687 restraints weight = 10490.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.126069 restraints weight = 6432.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.127626 restraints weight = 4495.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.128685 restraints weight = 3502.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.129277 restraints weight = 2921.985| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5931 Z= 0.125 Angle : 0.689 10.451 8028 Z= 0.326 Chirality : 0.042 0.157 916 Planarity : 0.004 0.043 1040 Dihedral : 4.970 43.029 844 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.06 % Allowed : 23.83 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.72 (0.32), residues: 740 helix: -0.02 (0.27), residues: 381 sheet: -0.66 (0.60), residues: 65 loop : -0.89 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 86 TYR 0.009 0.001 TYR A 503 PHE 0.033 0.002 PHE A 308 TRP 0.023 0.001 TRP A 103 HIS 0.002 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 5930) covalent geometry : angle 0.68934 / 0.33 ( 8026) SS BOND : bond 0.00347 / 0.22 ( 1) SS BOND : angle 0.75976 / 0.30 ( 2) hydrogen bonds : bond 0.03460 / 2.31 ( 260) hydrogen bonds : angle 4.06033 / 2.96 ( 738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 175 ARG cc_start: 0.7002 (ptp-170) cc_final: 0.6796 (mpp80) REVERT: A 191 MET cc_start: 0.8068 (tpp) cc_final: 0.7667 (tpp) REVERT: A 232 ASN cc_start: 0.8264 (m-40) cc_final: 0.7688 (t0) REVERT: A 249 ARG cc_start: 0.6161 (mmt180) cc_final: 0.5724 (mmt180) REVERT: A 307 ARG cc_start: 0.7823 (mmm160) cc_final: 0.7600 (tpm170) REVERT: B 699 LEU cc_start: 0.6967 (mt) cc_final: 0.6197 (pp) REVERT: C 65 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8473 (ttmm) outliers start: 19 outliers final: 16 residues processed: 158 average time/residue: 0.1075 time to fit residues: 20.9727 Evaluate side-chains 161 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 41 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 1 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 42 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 overall best weight: 0.2656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.142013 restraints weight = 10616.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.143973 restraints weight = 21051.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144347 restraints weight = 12261.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144473 restraints weight = 8132.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145055 restraints weight = 7344.505| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 5931 Z= 0.123 Angle : 0.705 10.496 8028 Z= 0.336 Chirality : 0.042 0.151 916 Planarity : 0.005 0.090 1040 Dihedral : 4.877 37.030 844 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.58 % Allowed : 25.76 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.32), residues: 740 helix: 0.10 (0.27), residues: 380 sheet: -0.58 (0.61), residues: 65 loop : -0.80 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 543 TYR 0.009 0.001 TYR A 503 PHE 0.034 0.002 PHE A 308 TRP 0.017 0.001 TRP A 103 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 5930) covalent geometry : angle 0.70504 / 0.34 ( 8026) SS BOND : bond 0.00284 / 0.18 ( 1) SS BOND : angle 0.65130 / 0.25 ( 2) hydrogen bonds : bond 0.03477 / 2.32 ( 260) hydrogen bonds : angle 4.08111 / 3.00 ( 738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.229 Fit side-chains revert: symmetry clash REVERT: A 249 ARG cc_start: 0.6159 (mmt180) cc_final: 0.5929 (mmt180) REVERT: A 310 ARG cc_start: 0.6978 (mmm-85) cc_final: 0.6259 (tpp80) REVERT: B 699 LEU cc_start: 0.6648 (mt) cc_final: 0.6095 (pp) REVERT: C 35 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8153 (mpp) REVERT: C 65 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8415 (ttmm) outliers start: 16 outliers final: 15 residues processed: 154 average time/residue: 0.0882 time to fit residues: 16.8597 Evaluate side-chains 159 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 2 optimal weight: 7.9990 chunk 6 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 chunk 65 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 66 optimal weight: 0.4980 chunk 64 optimal weight: 0.5980 chunk 67 optimal weight: 0.4980 chunk 15 optimal weight: 0.1980 chunk 48 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.168800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137815 restraints weight = 10692.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.140841 restraints weight = 19263.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141356 restraints weight = 7713.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141721 restraints weight = 5629.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.142159 restraints weight = 5261.032| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5931 Z= 0.134 Angle : 0.722 10.388 8028 Z= 0.347 Chirality : 0.042 0.153 916 Planarity : 0.006 0.089 1040 Dihedral : 4.868 35.507 844 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.74 % Allowed : 25.44 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.32), residues: 740 helix: 0.12 (0.27), residues: 380 sheet: -0.59 (0.61), residues: 65 loop : -0.74 (0.39), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 201 TYR 0.009 0.001 TYR A 503 PHE 0.033 0.002 PHE A 308 TRP 0.015 0.001 TRP A 103 HIS 0.003 0.001 HIS A 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 ( 5930) covalent geometry : angle 0.72169 / 0.35 ( 8026) SS BOND : bond 0.00330 / 0.21 ( 1) SS BOND : angle 0.77841 / 0.31 ( 2) hydrogen bonds : bond 0.03499 / 2.33 ( 260) hydrogen bonds : angle 4.09972 / 3.00 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 249 ARG cc_start: 0.6297 (mmt180) cc_final: 0.5915 (mmt180) REVERT: A 310 ARG cc_start: 0.7078 (mmm-85) cc_final: 0.6313 (tpp80) REVERT: A 387 SER cc_start: 0.8940 (t) cc_final: 0.8691 (p) REVERT: B 652 ASN cc_start: 0.7000 (m110) cc_final: 0.6545 (m110) REVERT: B 699 LEU cc_start: 0.6784 (mt) cc_final: 0.6251 (pp) REVERT: C 35 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8220 (mpp) REVERT: C 80 TYR cc_start: 0.8196 (m-80) cc_final: 0.7941 (m-80) outliers start: 17 outliers final: 16 residues processed: 146 average time/residue: 0.0888 time to fit residues: 16.1812 Evaluate side-chains 156 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 642 GLU Chi-restraints excluded: chain B residue 654 VAL Chi-restraints excluded: chain B residue 687 TYR Chi-restraints excluded: chain B residue 691 THR Chi-restraints excluded: chain C residue 35 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 47 optimal weight: 0.0040 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 0.0270 chunk 71 optimal weight: 0.6980 overall best weight: 0.4850 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.170002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141155 restraints weight = 10572.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.143362 restraints weight = 21959.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.143616 restraints weight = 10668.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.143568 restraints weight = 7414.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144086 restraints weight = 6827.943| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5931 Z= 0.146 Angle : 0.730 11.917 8028 Z= 0.352 Chirality : 0.042 0.145 916 Planarity : 0.005 0.072 1040 Dihedral : 4.922 34.244 844 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.90 % Allowed : 25.28 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.32), residues: 740 helix: 0.18 (0.27), residues: 376 sheet: -0.52 (0.61), residues: 65 loop : -0.70 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 201 TYR 0.009 0.001 TYR B 687 PHE 0.036 0.002 PHE A 308 TRP 0.015 0.001 TRP A 103 HIS 0.007 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 5930) covalent geometry : angle 0.72967 / 0.35 ( 8026) SS BOND : bond 0.00400 / 0.25 ( 1) SS BOND : angle 0.89506 / 0.37 ( 2) hydrogen bonds : bond 0.03628 / 2.44 ( 260) hydrogen bonds : angle 4.14580 / 3.02 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1267.58 seconds wall clock time: 22 minutes 28.40 seconds (1348.40 seconds total)