Starting phenix.real_space_refine on Tue Feb 3 17:40:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1b_61970/02_2026/9k1b_61970.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1b_61970/02_2026/9k1b_61970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k1b_61970/02_2026/9k1b_61970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1b_61970/02_2026/9k1b_61970.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k1b_61970/02_2026/9k1b_61970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1b_61970/02_2026/9k1b_61970.map" } resolution = 3.34 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= -0.004 sd= 0.073 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: 6 Type Number sf(0) Gaussians S 39 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 3704 2.51 5 N 883 2.21 5 O 985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5614 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4036 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 28, 'TRANS': 509} Chain breaks: 1 Unresolved non-hydrogen bonds: 264 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'PHE:plan': 7, 'HIS:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 6, 'ARG:plan': 7, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 179 Chain: "H" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 851 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 51 Chain: "L" Number of atoms: 717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 717 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 101} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 10 Unusual residues: {' CL': 1, ' NA': 2, 'TAU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.00, per 1000 atoms: 0.18 Number of scatterers: 5614 At special positions: 0 Unit cell: (84.315, 88.695, 105.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 39 16.00 Na 2 11.00 O 985 8.00 N 883 7.00 C 3704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 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: 0.38 Conformation dependent library (CDL) restraints added in 330.4 milliseconds 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1386 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 6 sheets defined 58.1% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 46 through 59 removed outlier: 3.600A pdb=" N PHE A 50 " --> pdb=" O SER A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.931A pdb=" N TYR A 69 " --> pdb=" O TRP A 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 78 removed outlier: 4.277A pdb=" N ALA A 78 " --> pdb=" O GLY A 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 75 through 78' Processing helix chain 'A' and resid 79 through 105 removed outlier: 5.903A pdb=" N LEU A 92 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 121 through 153 removed outlier: 3.940A pdb=" N TYR A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ILE A 139 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 141 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LEU A 142 " --> pdb=" O TYR A 138 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.921A pdb=" N HIS A 161 " --> pdb=" O PRO A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 removed outlier: 4.249A pdb=" N LYS A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 203 removed outlier: 3.863A pdb=" N TRP A 199 " --> pdb=" O VAL A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 236 removed outlier: 3.852A pdb=" N CYS A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TRP A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 removed outlier: 3.782A pdb=" N PHE A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 269 through 279 removed outlier: 3.586A pdb=" N GLY A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 287 Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.750A pdb=" N ALA A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 removed outlier: 3.801A pdb=" N TYR A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 356 removed outlier: 3.804A pdb=" N GLY A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 347 " --> pdb=" O ALA A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 362 removed outlier: 3.510A pdb=" N VAL A 362 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 379 Proline residue: A 375 - end of helix Processing helix chain 'A' and resid 383 through 416 removed outlier: 3.953A pdb=" N TRP A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE A 392 " --> pdb=" O SER A 388 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N SER A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP A 416 " --> pdb=" O THR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 444 removed outlier: 3.761A pdb=" N GLU A 429 " --> pdb=" O GLY A 425 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 450 through 462 removed outlier: 3.918A pdb=" N VAL A 454 " --> pdb=" O GLY A 450 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 457 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 482 removed outlier: 3.884A pdb=" N LEU A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 510 through 526 removed outlier: 3.755A pdb=" N LEU A 524 " --> pdb=" O PHE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 555 removed outlier: 3.777A pdb=" N SER A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 567 removed outlier: 3.571A pdb=" N ILE A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 removed outlier: 3.533A pdb=" N LYS A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.969A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.658A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.198A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TRP L 36 " --> pdb=" O TRP L 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.822A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 933 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: 0.54 Time building geometry restraints manager: 0.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 845 1.31 - 1.44: 1744 1.44 - 1.57: 3133 1.57 - 1.69: 1 1.69 - 1.82: 55 Bond restraints: 5778 Sorted by residual: bond pdb=" N GLU A 107 " pdb=" CA GLU A 107 " ideal model delta sigma weight residual 1.456 1.398 0.059 1.16e-02 7.43e+03 2.55e+01 bond pdb=" C GLU A 107 " pdb=" O GLU A 107 " ideal model delta sigma weight residual 1.233 1.185 0.048 1.17e-02 7.31e+03 1.68e+01 bond pdb=" C ASP A 416 " pdb=" O ASP A 416 " ideal model delta sigma weight residual 1.236 1.198 0.038 1.28e-02 6.10e+03 8.72e+00 bond pdb=" O3 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.478 1.429 0.049 2.00e-02 2.50e+03 5.92e+00 bond pdb=" O2 TAU A 701 " pdb=" S TAU A 701 " ideal model delta sigma weight residual 1.477 1.525 -0.048 2.00e-02 2.50e+03 5.77e+00 ... (remaining 5773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 7785 2.19 - 4.38: 124 4.38 - 6.57: 11 6.57 - 8.77: 3 8.77 - 10.96: 1 Bond angle restraints: 7924 Sorted by residual: angle pdb=" CG1 VAL A 562 " pdb=" CB VAL A 562 " pdb=" CG2 VAL A 562 " ideal model delta sigma weight residual 110.80 121.76 -10.96 2.20e+00 2.07e-01 2.48e+01 angle pdb=" N GLU A 107 " pdb=" CA GLU A 107 " pdb=" CB GLU A 107 " ideal model delta sigma weight residual 111.46 104.28 7.18 1.54e+00 4.22e-01 2.17e+01 angle pdb=" CA VAL A 562 " pdb=" CB VAL A 562 " pdb=" CG2 VAL A 562 " ideal model delta sigma weight residual 110.40 118.23 -7.83 1.70e+00 3.46e-01 2.12e+01 angle pdb=" CA VAL A 562 " pdb=" CB VAL A 562 " pdb=" CG1 VAL A 562 " ideal model delta sigma weight residual 110.40 116.17 -5.77 1.70e+00 3.46e-01 1.15e+01 angle pdb=" N CYS A 305 " pdb=" CA CYS A 305 " pdb=" C CYS A 305 " ideal model delta sigma weight residual 112.93 109.56 3.37 1.12e+00 7.97e-01 9.04e+00 ... (remaining 7919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.89: 2898 12.89 - 25.78: 240 25.78 - 38.67: 79 38.67 - 51.55: 20 51.55 - 64.44: 10 Dihedral angle restraints: 3247 sinusoidal: 1061 harmonic: 2186 Sorted by residual: dihedral pdb=" CB CYS A 162 " pdb=" SG CYS A 162 " pdb=" SG CYS A 171 " pdb=" CB CYS A 171 " ideal model delta sinusoidal sigma weight residual -86.00 -127.10 41.10 1 1.00e+01 1.00e-02 2.37e+01 dihedral pdb=" CA SER A 205 " pdb=" C SER A 205 " pdb=" N LEU A 206 " pdb=" CA LEU A 206 " ideal model delta harmonic sigma weight residual 180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE A 58 " pdb=" C PHE A 58 " pdb=" N VAL A 59 " pdb=" CA VAL A 59 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 3244 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.308: 908 0.308 - 0.617: 0 0.617 - 0.925: 0 0.925 - 1.233: 0 1.233 - 1.542: 1 Chirality restraints: 909 Sorted by residual: chirality pdb=" CB VAL A 562 " pdb=" CA VAL A 562 " pdb=" CG1 VAL A 562 " pdb=" CG2 VAL A 562 " both_signs ideal model delta sigma weight residual False -2.63 -1.09 -1.54 2.00e-01 2.50e+01 5.94e+01 chirality pdb=" CB VAL L 59 " pdb=" CA VAL L 59 " pdb=" CG1 VAL L 59 " pdb=" CG2 VAL L 59 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 ... (remaining 906 not shown) Planarity restraints: 980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP A 199 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C TRP A 199 " -0.039 2.00e-02 2.50e+03 pdb=" O TRP A 199 " 0.015 2.00e-02 2.50e+03 pdb=" N GLU A 200 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 59 " -0.037 5.00e-02 4.00e+02 5.57e-02 4.96e+00 pdb=" N PRO L 60 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO L 60 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 60 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 87 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.88e+00 pdb=" C LEU A 87 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU A 87 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE A 88 " -0.013 2.00e-02 2.50e+03 ... (remaining 977 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 13 2.43 - 3.04: 3624 3.04 - 3.66: 8108 3.66 - 4.28: 12075 4.28 - 4.90: 20678 Nonbonded interactions: 44498 Sorted by model distance: nonbonded pdb=" OD1 ASP A 401 " pdb="NA NA A 702 " model vdw 1.807 2.470 nonbonded pdb=" OG SER A 402 " pdb="NA NA A 702 " model vdw 1.937 2.470 nonbonded pdb=" OG SER A 301 " pdb="NA NA A 703 " model vdw 2.012 2.470 nonbonded pdb=" O PHE A 58 " pdb=" O1 TAU A 701 " model vdw 2.020 3.040 nonbonded pdb=" O VAL A 59 " pdb="NA NA A 702 " model vdw 2.060 2.470 ... (remaining 44493 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.300 Find NCS groups from input model: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 7.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 0.084 5781 Z= 0.201 Angle : 0.701 10.957 7930 Z= 0.391 Chirality : 0.066 1.542 909 Planarity : 0.005 0.063 980 Dihedral : 12.018 64.441 1852 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.37 % Allowed : 9.61 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.12 (0.31), residues: 755 helix: 0.08 (0.27), residues: 366 sheet: 0.54 (0.50), residues: 118 loop : -0.38 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG H 104 TYR 0.017 0.001 TYR A 69 PHE 0.023 0.002 PHE L 63 TRP 0.020 0.002 TRP A 541 HIS 0.005 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 5778) covalent geometry : angle 0.70075 ( 7924) SS BOND : bond 0.00346 ( 3) SS BOND : angle 0.90513 ( 6) hydrogen bonds : bond 0.15770 ( 327) hydrogen bonds : angle 6.30764 ( 933) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.191 Fit side-chains REVERT: A 107 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: A 416 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.6959 (m-30) REVERT: A 487 ARG cc_start: 0.8318 (ttp-110) cc_final: 0.7925 (mtp85) REVERT: L 95 TYR cc_start: 0.8325 (m-80) cc_final: 0.8084 (m-80) outliers start: 2 outliers final: 0 residues processed: 105 average time/residue: 0.0567 time to fit residues: 7.9039 Evaluate side-chains 88 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 GLU Chi-restraints excluded: chain A residue 416 ASP 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: 0.2980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.144105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.125453 restraints weight = 8087.055| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.04 r_work: 0.3447 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5781 Z= 0.120 Angle : 0.570 8.014 7930 Z= 0.298 Chirality : 0.041 0.140 909 Planarity : 0.005 0.044 980 Dihedral : 5.847 55.040 824 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.40 % Allowed : 10.54 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.78 (0.32), residues: 755 helix: 1.16 (0.28), residues: 368 sheet: 0.66 (0.51), residues: 111 loop : -0.31 (0.41), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 104 TYR 0.008 0.001 TYR H 60 PHE 0.012 0.001 PHE A 474 TRP 0.020 0.002 TRP A 470 HIS 0.003 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 5778) covalent geometry : angle 0.56957 ( 7924) SS BOND : bond 0.00607 ( 3) SS BOND : angle 0.93221 ( 6) hydrogen bonds : bond 0.04188 ( 327) hydrogen bonds : angle 4.70982 ( 933) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.141 Fit side-chains REVERT: A 353 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8240 (tp40) REVERT: A 459 ASP cc_start: 0.8930 (t70) cc_final: 0.8723 (t0) REVERT: A 487 ARG cc_start: 0.8150 (ttp-110) cc_final: 0.7775 (mtp85) REVERT: L 95 TYR cc_start: 0.8473 (m-80) cc_final: 0.8268 (m-80) outliers start: 13 outliers final: 8 residues processed: 99 average time/residue: 0.0710 time to fit residues: 9.4429 Evaluate side-chains 89 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 57 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.139096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120084 restraints weight = 7975.625| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.08 r_work: 0.3349 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5781 Z= 0.127 Angle : 0.562 6.986 7930 Z= 0.289 Chirality : 0.041 0.158 909 Planarity : 0.004 0.041 980 Dihedral : 4.694 50.491 819 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.77 % Allowed : 10.17 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.02 (0.32), residues: 755 helix: 1.47 (0.28), residues: 369 sheet: 0.54 (0.50), residues: 115 loop : -0.28 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 104 TYR 0.009 0.001 TYR L 95 PHE 0.016 0.001 PHE A 79 TRP 0.017 0.001 TRP A 470 HIS 0.002 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 5778) covalent geometry : angle 0.56133 ( 7924) SS BOND : bond 0.00604 ( 3) SS BOND : angle 0.94357 ( 6) hydrogen bonds : bond 0.04107 ( 327) hydrogen bonds : angle 4.48411 ( 933) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.258 Fit side-chains REVERT: A 353 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8154 (tp40) REVERT: A 459 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8777 (t0) REVERT: L 95 TYR cc_start: 0.8593 (m-80) cc_final: 0.8285 (m-80) outliers start: 15 outliers final: 10 residues processed: 97 average time/residue: 0.0761 time to fit residues: 10.0426 Evaluate side-chains 96 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 552 SER Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 107 ASP Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 0.1980 chunk 50 optimal weight: 0.0570 chunk 23 optimal weight: 0.8980 chunk 24 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.142508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123480 restraints weight = 8020.599| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.11 r_work: 0.3399 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 5781 Z= 0.096 Angle : 0.509 6.831 7930 Z= 0.258 Chirality : 0.039 0.150 909 Planarity : 0.004 0.039 980 Dihedral : 4.287 46.100 819 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.48 % Allowed : 12.57 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.24 (0.32), residues: 755 helix: 1.73 (0.28), residues: 373 sheet: 0.47 (0.50), residues: 115 loop : -0.25 (0.41), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 67 TYR 0.014 0.001 TYR A 578 PHE 0.010 0.001 PHE A 79 TRP 0.015 0.001 TRP A 470 HIS 0.002 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 5778) covalent geometry : angle 0.50896 ( 7924) SS BOND : bond 0.00490 ( 3) SS BOND : angle 0.82349 ( 6) hydrogen bonds : bond 0.03303 ( 327) hydrogen bonds : angle 4.22586 ( 933) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.214 Fit side-chains REVERT: A 459 ASP cc_start: 0.9071 (OUTLIER) cc_final: 0.8793 (t0) REVERT: A 549 LEU cc_start: 0.8151 (tp) cc_final: 0.7864 (mt) REVERT: H 56 ARG cc_start: 0.8585 (mtp-110) cc_final: 0.8310 (mtp-110) REVERT: L 90 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8073 (tt0) outliers start: 8 outliers final: 5 residues processed: 100 average time/residue: 0.0608 time to fit residues: 8.6520 Evaluate side-chains 94 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain A residue 565 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118193 restraints weight = 8205.476| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.12 r_work: 0.3339 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5781 Z= 0.149 Angle : 0.570 6.892 7930 Z= 0.290 Chirality : 0.042 0.159 909 Planarity : 0.004 0.045 980 Dihedral : 4.551 50.694 819 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.03 % Allowed : 13.49 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.04 (0.32), residues: 755 helix: 1.55 (0.28), residues: 375 sheet: 0.38 (0.51), residues: 115 loop : -0.32 (0.40), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 263 TYR 0.015 0.001 TYR L 50 PHE 0.018 0.001 PHE A 79 TRP 0.014 0.001 TRP A 470 HIS 0.002 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5778) covalent geometry : angle 0.56962 ( 7924) SS BOND : bond 0.00640 ( 3) SS BOND : angle 1.01824 ( 6) hydrogen bonds : bond 0.04149 ( 327) hydrogen bonds : angle 4.39050 ( 933) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.218 Fit side-chains REVERT: H 60 TYR cc_start: 0.9034 (m-80) cc_final: 0.8756 (m-80) REVERT: L 95 TYR cc_start: 0.8619 (m-80) cc_final: 0.8260 (m-80) outliers start: 11 outliers final: 9 residues processed: 92 average time/residue: 0.0748 time to fit residues: 9.2775 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 107 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 30 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 70 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.140209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121083 restraints weight = 8050.906| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.13 r_work: 0.3376 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5781 Z= 0.106 Angle : 0.521 7.337 7930 Z= 0.262 Chirality : 0.040 0.155 909 Planarity : 0.004 0.044 980 Dihedral : 4.356 49.790 819 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.22 % Allowed : 13.86 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.12 (0.32), residues: 755 helix: 1.71 (0.28), residues: 375 sheet: 0.34 (0.51), residues: 115 loop : -0.40 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 56 TYR 0.010 0.001 TYR A 315 PHE 0.012 0.001 PHE A 79 TRP 0.013 0.001 TRP A 470 HIS 0.001 0.000 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5778) covalent geometry : angle 0.52074 ( 7924) SS BOND : bond 0.00509 ( 3) SS BOND : angle 0.84465 ( 6) hydrogen bonds : bond 0.03454 ( 327) hydrogen bonds : angle 4.20865 ( 933) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.253 Fit side-chains REVERT: H 60 TYR cc_start: 0.8964 (m-80) cc_final: 0.8719 (m-80) REVERT: L 90 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8058 (tt0) REVERT: L 95 TYR cc_start: 0.8533 (m-80) cc_final: 0.8294 (m-80) outliers start: 12 outliers final: 11 residues processed: 95 average time/residue: 0.0693 time to fit residues: 9.1541 Evaluate side-chains 96 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 8 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 51 optimal weight: 0.0980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.0470 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126008 restraints weight = 8160.336| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.06 r_work: 0.3436 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5781 Z= 0.096 Angle : 0.501 7.106 7930 Z= 0.250 Chirality : 0.039 0.150 909 Planarity : 0.004 0.044 980 Dihedral : 4.122 46.108 819 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.85 % Allowed : 14.97 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.09 (0.32), residues: 755 helix: 1.71 (0.28), residues: 383 sheet: 0.34 (0.51), residues: 110 loop : -0.53 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 56 TYR 0.017 0.001 TYR A 578 PHE 0.011 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 5778) covalent geometry : angle 0.50033 ( 7924) SS BOND : bond 0.00413 ( 3) SS BOND : angle 0.87026 ( 6) hydrogen bonds : bond 0.03208 ( 327) hydrogen bonds : angle 4.08162 ( 933) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.217 Fit side-chains REVERT: A 491 ASP cc_start: 0.8425 (m-30) cc_final: 0.8158 (m-30) REVERT: A 549 LEU cc_start: 0.8133 (tp) cc_final: 0.7828 (mt) REVERT: H 60 TYR cc_start: 0.8937 (m-80) cc_final: 0.8718 (m-80) REVERT: L 90 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8064 (tt0) REVERT: L 95 TYR cc_start: 0.8554 (m-80) cc_final: 0.8324 (m-80) outliers start: 10 outliers final: 9 residues processed: 95 average time/residue: 0.0602 time to fit residues: 8.3122 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 3 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118688 restraints weight = 8153.760| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.09 r_work: 0.3335 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5781 Z= 0.134 Angle : 0.549 8.279 7930 Z= 0.276 Chirality : 0.041 0.150 909 Planarity : 0.004 0.046 980 Dihedral : 4.344 49.288 819 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.77 % Allowed : 14.42 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.92 (0.32), residues: 755 helix: 1.55 (0.28), residues: 382 sheet: 0.30 (0.50), residues: 115 loop : -0.58 (0.40), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 67 TYR 0.014 0.001 TYR L 50 PHE 0.016 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.001 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 5778) covalent geometry : angle 0.54894 ( 7924) SS BOND : bond 0.00548 ( 3) SS BOND : angle 0.95306 ( 6) hydrogen bonds : bond 0.03825 ( 327) hydrogen bonds : angle 4.24495 ( 933) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.230 Fit side-chains REVERT: A 491 ASP cc_start: 0.8457 (m-30) cc_final: 0.8052 (m-30) REVERT: H 60 TYR cc_start: 0.9005 (m-80) cc_final: 0.8719 (m-80) REVERT: L 90 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8440 (tt0) REVERT: L 95 TYR cc_start: 0.8573 (m-80) cc_final: 0.8368 (m-80) outliers start: 15 outliers final: 13 residues processed: 94 average time/residue: 0.0634 time to fit residues: 8.5999 Evaluate side-chains 94 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 56 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.136714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118267 restraints weight = 8213.573| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.10 r_work: 0.3327 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5781 Z= 0.137 Angle : 0.550 9.075 7930 Z= 0.277 Chirality : 0.041 0.151 909 Planarity : 0.004 0.045 980 Dihedral : 4.453 52.799 819 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.77 % Allowed : 14.42 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 0.83 (0.32), residues: 755 helix: 1.49 (0.28), residues: 382 sheet: 0.24 (0.49), residues: 115 loop : -0.65 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 177 TYR 0.018 0.001 TYR A 578 PHE 0.016 0.001 PHE A 79 TRP 0.013 0.001 TRP A 199 HIS 0.001 0.001 HIS H 80 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5778) covalent geometry : angle 0.54957 ( 7924) SS BOND : bond 0.00566 ( 3) SS BOND : angle 0.94565 ( 6) hydrogen bonds : bond 0.03853 ( 327) hydrogen bonds : angle 4.28386 ( 933) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.228 Fit side-chains REVERT: A 578 TYR cc_start: 0.8020 (t80) cc_final: 0.7812 (t80) REVERT: A 581 THR cc_start: 0.8818 (m) cc_final: 0.8403 (p) REVERT: H 60 TYR cc_start: 0.9020 (m-80) cc_final: 0.8744 (m-80) REVERT: L 90 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8434 (tt0) outliers start: 15 outliers final: 14 residues processed: 89 average time/residue: 0.0537 time to fit residues: 7.1960 Evaluate side-chains 93 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 1 optimal weight: 5.9990 chunk 72 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 59 optimal weight: 0.0000 chunk 48 optimal weight: 0.9980 chunk 69 optimal weight: 0.4980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.140139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.121664 restraints weight = 8287.850| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.14 r_work: 0.3371 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 5781 Z= 0.099 Angle : 0.514 9.198 7930 Z= 0.255 Chirality : 0.039 0.150 909 Planarity : 0.004 0.045 980 Dihedral : 4.198 49.737 819 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.22 % Allowed : 15.16 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: 1.00 (0.32), residues: 755 helix: 1.65 (0.28), residues: 383 sheet: 0.25 (0.50), residues: 110 loop : -0.57 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 102 TYR 0.017 0.001 TYR A 578 PHE 0.011 0.001 PHE A 79 TRP 0.012 0.001 TRP A 470 HIS 0.001 0.000 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 5778) covalent geometry : angle 0.51401 ( 7924) SS BOND : bond 0.00410 ( 3) SS BOND : angle 0.82757 ( 6) hydrogen bonds : bond 0.03227 ( 327) hydrogen bonds : angle 4.11234 ( 933) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1510 Ramachandran restraints generated. 755 Oldfield, 0 Emsley, 755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.254 Fit side-chains REVERT: A 361 ASP cc_start: 0.7578 (m-30) cc_final: 0.7111 (t0) REVERT: A 491 ASP cc_start: 0.8378 (m-30) cc_final: 0.7984 (m-30) REVERT: A 549 LEU cc_start: 0.8134 (tp) cc_final: 0.7877 (mt) REVERT: A 581 THR cc_start: 0.8775 (m) cc_final: 0.8346 (p) REVERT: H 60 TYR cc_start: 0.8954 (m-80) cc_final: 0.8734 (m-80) REVERT: H 100 GLU cc_start: 0.8894 (tp30) cc_final: 0.8508 (tp30) REVERT: L 90 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8074 (tt0) REVERT: L 95 TYR cc_start: 0.8509 (m-80) cc_final: 0.8239 (m-80) outliers start: 12 outliers final: 11 residues processed: 96 average time/residue: 0.0590 time to fit residues: 8.2597 Evaluate side-chains 94 residues out of total 649 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 TYR Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 528 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 86 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 28 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.136864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118353 restraints weight = 8204.995| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.12 r_work: 0.3331 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5781 Z= 0.138 Angle : 0.576 13.083 7930 Z= 0.284 Chirality : 0.041 0.149 909 Planarity : 0.004 0.047 980 Dihedral : 4.383 52.607 819 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.22 % Allowed : 15.53 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.32), residues: 755 helix: 1.45 (0.28), residues: 383 sheet: 0.24 (0.51), residues: 110 loop : -0.62 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 177 TYR 0.015 0.001 TYR L 50 PHE 0.015 0.001 PHE A 79 TRP 0.013 0.001 TRP A 199 HIS 0.001 0.001 HIS L 35 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5778) covalent geometry : angle 0.57532 ( 7924) SS BOND : bond 0.00524 ( 3) SS BOND : angle 0.90714 ( 6) hydrogen bonds : bond 0.03834 ( 327) hydrogen bonds : angle 4.26836 ( 933) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1447.80 seconds wall clock time: 25 minutes 32.70 seconds (1532.70 seconds total)