Starting phenix.real_space_refine on Fri Oct 10 16:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u5q_41930/10_2025/8u5q_41930.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u5q_41930/10_2025/8u5q_41930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u5q_41930/10_2025/8u5q_41930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u5q_41930/10_2025/8u5q_41930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u5q_41930/10_2025/8u5q_41930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u5q_41930/10_2025/8u5q_41930.map" } resolution = 2.4 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 5298 2.51 5 N 1218 2.21 5 O 1334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7896 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3935 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 482} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 3935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 502, 3935 Classifications: {'peptide': 502} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 482} Chain breaks: 4 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.79, per 1000 atoms: 0.23 Number of scatterers: 7896 At special positions: 0 Unit cell: (122.999, 100.837, 76.4589, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 1334 8.00 N 1218 7.00 C 5298 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.62 Conformation dependent library (CDL) restraints added in 354.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 0 sheets defined 89.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.695A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 removed outlier: 3.662A pdb=" N VAL A 98 " --> pdb=" O PHE A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.599A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.660A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 196 removed outlier: 4.299A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 removed outlier: 3.999A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 238 through 264 removed outlier: 4.180A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.190A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.654A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 433 removed outlier: 3.871A pdb=" N ASN A 417 " --> pdb=" O MET A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 472 Processing helix chain 'A' and resid 655 through 680 removed outlier: 4.265A pdb=" N PHE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA A 671 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS A 676 " --> pdb=" O ASN A 672 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 711 removed outlier: 5.676A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 41 through 62 Processing helix chain 'C' and resid 66 through 80 removed outlier: 3.688A pdb=" N LYS C 71 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLY C 72 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU C 73 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.666A pdb=" N VAL C 98 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 125 removed outlier: 3.608A pdb=" N LEU C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 143 Proline residue: C 138 - end of helix Processing helix chain 'C' and resid 149 through 159 removed outlier: 3.660A pdb=" N ILE C 153 " --> pdb=" O LEU C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 165 Processing helix chain 'C' and resid 166 through 196 removed outlier: 4.295A pdb=" N TYR C 170 " --> pdb=" O LEU C 166 " (cutoff:3.500A) Proline residue: C 174 - end of helix Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 202 through 216 removed outlier: 4.000A pdb=" N ILE C 206 " --> pdb=" O ASN C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 234 Processing helix chain 'C' and resid 238 through 264 removed outlier: 4.180A pdb=" N ASN C 243 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE C 244 " --> pdb=" O TYR C 240 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLY C 254 " --> pdb=" O ASN C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 288 Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 306 through 322 Processing helix chain 'C' and resid 326 through 337 removed outlier: 4.195A pdb=" N ALA C 330 " --> pdb=" O ALA C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 367 removed outlier: 3.659A pdb=" N ALA C 355 " --> pdb=" O THR C 351 " (cutoff:3.500A) Proline residue: C 356 - end of helix Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 371 through 404 Processing helix chain 'C' and resid 405 through 409 Processing helix chain 'C' and resid 411 through 433 removed outlier: 3.871A pdb=" N ASN C 417 " --> pdb=" O MET C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 472 Processing helix chain 'C' and resid 655 through 680 removed outlier: 4.294A pdb=" N ILE C 667 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 711 removed outlier: 5.691A pdb=" N GLY C 704 " --> pdb=" O ASN C 700 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE C 705 " --> pdb=" O PHE C 701 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 706 " --> pdb=" O GLY C 702 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1881 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.02 Time building geometry restraints manager: 0.83 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: 2314 1.34 - 1.46: 1845 1.46 - 1.58: 3859 1.58 - 1.70: 0 1.70 - 1.81: 74 Bond restraints: 8092 Sorted by residual: bond pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.433 1.364 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C1 IAC C 901 " pdb=" C7 IAC C 901 " ideal model delta sigma weight residual 1.433 1.364 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" C IAC A 901 " pdb=" C1 IAC A 901 " ideal model delta sigma weight residual 1.414 1.363 0.051 2.00e-02 2.50e+03 6.49e+00 bond pdb=" C IAC C 901 " pdb=" C1 IAC C 901 " ideal model delta sigma weight residual 1.414 1.365 0.049 2.00e-02 2.50e+03 5.99e+00 bond pdb=" C17 IAC C 901 " pdb=" C7 IAC C 901 " ideal model delta sigma weight residual 1.487 1.530 -0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 8087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 10782 2.71 - 5.42: 186 5.42 - 8.12: 21 8.12 - 10.83: 3 10.83 - 13.54: 4 Bond angle restraints: 10996 Sorted by residual: angle pdb=" C SER A 675 " pdb=" N CYS A 676 " pdb=" CA CYS A 676 " ideal model delta sigma weight residual 121.52 112.76 8.76 1.84e+00 2.95e-01 2.27e+01 angle pdb=" C17 IAC C 901 " pdb=" C7 IAC C 901 " pdb=" C8 IAC C 901 " ideal model delta sigma weight residual 127.34 113.80 13.54 3.00e+00 1.11e-01 2.04e+01 angle pdb=" C17 IAC A 901 " pdb=" C7 IAC A 901 " pdb=" C8 IAC A 901 " ideal model delta sigma weight residual 127.34 113.87 13.47 3.00e+00 1.11e-01 2.02e+01 angle pdb=" C SER C 675 " pdb=" N CYS C 676 " pdb=" CA CYS C 676 " ideal model delta sigma weight residual 120.29 114.59 5.70 1.42e+00 4.96e-01 1.61e+01 angle pdb=" C1 IAC C 901 " pdb=" C7 IAC C 901 " pdb=" C17 IAC C 901 " ideal model delta sigma weight residual 126.92 138.66 -11.74 3.00e+00 1.11e-01 1.53e+01 ... (remaining 10991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 4368 16.99 - 33.98: 270 33.98 - 50.98: 37 50.98 - 67.97: 11 67.97 - 84.96: 6 Dihedral angle restraints: 4692 sinusoidal: 1776 harmonic: 2916 Sorted by residual: dihedral pdb=" CA PHE A 670 " pdb=" C PHE A 670 " pdb=" N ALA A 671 " pdb=" CA ALA A 671 " ideal model delta harmonic sigma weight residual -180.00 -151.18 -28.82 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA LEU A 233 " pdb=" C LEU A 233 " pdb=" N ASP A 234 " pdb=" CA ASP A 234 " ideal model delta harmonic sigma weight residual -180.00 -153.16 -26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU C 233 " pdb=" C LEU C 233 " pdb=" N ASP C 234 " pdb=" CA ASP C 234 " ideal model delta harmonic sigma weight residual -180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 4689 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 893 0.043 - 0.086: 322 0.086 - 0.128: 79 0.128 - 0.171: 9 0.171 - 0.214: 7 Chirality restraints: 1310 Sorted by residual: chirality pdb=" CA CYS A 676 " pdb=" N CYS A 676 " pdb=" C CYS A 676 " pdb=" CB CYS A 676 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CB VAL A 214 " pdb=" CA VAL A 214 " pdb=" CG1 VAL A 214 " pdb=" CG2 VAL A 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CB VAL C 214 " pdb=" CA VAL C 214 " pdb=" CG1 VAL C 214 " pdb=" CG2 VAL C 214 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1307 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " 0.038 2.00e-02 2.50e+03 2.01e-02 8.10e+00 pdb=" CG TYR A 320 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 320 " 0.038 2.00e-02 2.50e+03 2.00e-02 7.98e+00 pdb=" CG TYR C 320 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR C 320 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR C 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR C 320 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR C 320 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR C 320 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 221 " 0.025 2.00e-02 2.50e+03 2.13e-02 7.91e+00 pdb=" CG PHE C 221 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 221 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE C 221 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 221 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 221 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE C 221 " 0.004 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 3119 2.90 - 3.40: 8592 3.40 - 3.90: 14012 3.90 - 4.40: 16360 4.40 - 4.90: 26391 Nonbonded interactions: 68474 Sorted by model distance: nonbonded pdb=" OD1 ASN A 672 " pdb=" ND2 ASN A 700 " model vdw 2.402 3.120 nonbonded pdb=" O LEU C 454 " pdb=" OG1 THR C 457 " model vdw 2.415 3.040 nonbonded pdb=" O LEU A 454 " pdb=" OG1 THR A 457 " model vdw 2.417 3.040 nonbonded pdb=" OH TYR C 359 " pdb=" OD2 ASP C 385 " model vdw 2.417 3.040 nonbonded pdb=" OH TYR A 359 " pdb=" OD2 ASP A 385 " model vdw 2.417 3.040 ... (remaining 68469 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:8.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 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 : 0.006 0.069 8092 Z= 0.240 Angle : 0.896 13.539 10996 Z= 0.477 Chirality : 0.048 0.214 1310 Planarity : 0.006 0.066 1324 Dihedral : 12.123 84.962 2808 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.23 % Allowed : 1.39 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: -1.44 (0.24), residues: 984 helix: -0.82 (0.16), residues: 804 sheet: None (None), residues: 0 loop : -0.67 (0.48), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 130 TYR 0.038 0.004 TYR A 320 PHE 0.049 0.004 PHE C 221 TRP 0.024 0.004 TRP A 193 HIS 0.014 0.004 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00562 ( 8092) covalent geometry : angle 0.89617 (10996) hydrogen bonds : bond 0.16795 ( 635) hydrogen bonds : angle 7.10308 ( 1881) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 186 time to evaluate : 0.306 Fit side-chains REVERT: A 41 ARG cc_start: 0.7917 (mtp180) cc_final: 0.7714 (mmm-85) REVERT: A 319 LEU cc_start: 0.8660 (mm) cc_final: 0.8379 (tm) REVERT: A 347 MET cc_start: 0.8783 (tmm) cc_final: 0.8572 (tmm) REVERT: A 455 TYR cc_start: 0.4591 (m-10) cc_final: 0.3607 (t80) REVERT: C 347 MET cc_start: 0.8753 (tmm) cc_final: 0.8533 (tmm) REVERT: C 455 TYR cc_start: 0.4980 (m-10) cc_final: 0.3961 (t80) outliers start: 2 outliers final: 2 residues processed: 187 average time/residue: 0.5008 time to fit residues: 99.4953 Evaluate side-chains 123 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 505 HIS A 672 ASN C 143 GLN C 505 HIS C 672 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.131130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.099773 restraints weight = 14492.810| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.50 r_work: 0.3316 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8092 Z= 0.178 Angle : 0.661 9.019 10996 Z= 0.343 Chirality : 0.044 0.207 1310 Planarity : 0.005 0.034 1324 Dihedral : 5.568 48.407 1060 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 3.12 % Allowed : 9.47 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 1.01 (0.26), residues: 984 helix: 0.96 (0.17), residues: 802 sheet: None (None), residues: 0 loop : -0.28 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 295 TYR 0.024 0.002 TYR A 451 PHE 0.030 0.002 PHE C 221 TRP 0.019 0.002 TRP A 679 HIS 0.008 0.002 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 8092) covalent geometry : angle 0.66113 (10996) hydrogen bonds : bond 0.05634 ( 635) hydrogen bonds : angle 4.91650 ( 1881) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.307 Fit side-chains REVERT: A 41 ARG cc_start: 0.8425 (mtp180) cc_final: 0.8212 (mtm180) REVERT: A 164 GLU cc_start: 0.8733 (pm20) cc_final: 0.8496 (pm20) REVERT: A 255 SER cc_start: 0.8981 (t) cc_final: 0.8729 (m) REVERT: A 288 LEU cc_start: 0.8670 (tp) cc_final: 0.8323 (mp) REVERT: A 319 LEU cc_start: 0.8804 (mm) cc_final: 0.8174 (tp) REVERT: A 347 MET cc_start: 0.8444 (tmm) cc_final: 0.8098 (tmm) REVERT: A 359 TYR cc_start: 0.8837 (t80) cc_final: 0.8615 (t80) REVERT: A 455 TYR cc_start: 0.4421 (m-10) cc_final: 0.3566 (t80) REVERT: A 677 LEU cc_start: 0.8092 (tm) cc_final: 0.7858 (pp) REVERT: A 691 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: C 41 ARG cc_start: 0.8461 (mtm-85) cc_final: 0.8203 (mtm110) REVERT: C 90 MET cc_start: 0.9287 (tpp) cc_final: 0.9042 (mmm) REVERT: C 164 GLU cc_start: 0.8762 (pm20) cc_final: 0.8528 (pm20) REVERT: C 255 SER cc_start: 0.8962 (t) cc_final: 0.8725 (m) REVERT: C 288 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8301 (mp) REVERT: C 347 MET cc_start: 0.8422 (tmm) cc_final: 0.8090 (tmm) REVERT: C 358 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8409 (mtm) REVERT: C 455 TYR cc_start: 0.4347 (m-10) cc_final: 0.3545 (t80) REVERT: C 677 LEU cc_start: 0.8032 (tm) cc_final: 0.7619 (pp) REVERT: C 691 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7383 (tt0) outliers start: 27 outliers final: 4 residues processed: 175 average time/residue: 0.4148 time to fit residues: 77.7245 Evaluate side-chains 142 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 67 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 26 optimal weight: 0.1980 chunk 45 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 143 GLN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.130508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098974 restraints weight = 14298.207| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.48 r_work: 0.3301 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8092 Z= 0.181 Angle : 0.673 12.930 10996 Z= 0.330 Chirality : 0.043 0.220 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.844 31.653 1058 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.46 % Allowed : 12.70 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 1.74 (0.27), residues: 984 helix: 1.49 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.17 (0.50), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 295 TYR 0.024 0.002 TYR A 451 PHE 0.029 0.002 PHE A 221 TRP 0.020 0.002 TRP A 679 HIS 0.005 0.002 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 8092) covalent geometry : angle 0.67350 (10996) hydrogen bonds : bond 0.05267 ( 635) hydrogen bonds : angle 4.63318 ( 1881) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 0.217 Fit side-chains REVERT: A 164 GLU cc_start: 0.8802 (pm20) cc_final: 0.8470 (pm20) REVERT: A 288 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8368 (mp) REVERT: A 299 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 319 LEU cc_start: 0.8855 (mm) cc_final: 0.8202 (tp) REVERT: A 347 MET cc_start: 0.8530 (tmm) cc_final: 0.8229 (tmm) REVERT: A 677 LEU cc_start: 0.8119 (tm) cc_final: 0.7854 (pp) REVERT: A 691 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7521 (tt0) REVERT: C 41 ARG cc_start: 0.8517 (mtm-85) cc_final: 0.8223 (mtm110) REVERT: C 164 GLU cc_start: 0.8821 (pm20) cc_final: 0.8491 (pm20) REVERT: C 288 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8375 (mp) REVERT: C 299 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8413 (mt-10) REVERT: C 347 MET cc_start: 0.8555 (tmm) cc_final: 0.8267 (tmm) REVERT: C 358 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8362 (mtm) REVERT: C 677 LEU cc_start: 0.7927 (tm) cc_final: 0.7507 (pp) REVERT: C 691 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7553 (tt0) outliers start: 30 outliers final: 13 residues processed: 149 average time/residue: 0.4809 time to fit residues: 76.4177 Evaluate side-chains 135 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 358 MET Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 658 HIS Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 61 optimal weight: 0.0670 chunk 40 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 672 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.132030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100539 restraints weight = 14656.092| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.53 r_work: 0.3328 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8092 Z= 0.157 Angle : 0.652 12.779 10996 Z= 0.312 Chirality : 0.042 0.193 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.561 27.049 1058 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 3.58 % Allowed : 14.43 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 2.02 (0.27), residues: 984 helix: 1.70 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.18 (0.52), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 295 TYR 0.021 0.002 TYR A 451 PHE 0.028 0.002 PHE C 221 TRP 0.020 0.001 TRP A 679 HIS 0.009 0.002 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 8092) covalent geometry : angle 0.65195 (10996) hydrogen bonds : bond 0.04875 ( 635) hydrogen bonds : angle 4.45597 ( 1881) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.325 Fit side-chains REVERT: A 41 ARG cc_start: 0.8350 (mtm110) cc_final: 0.7937 (mtp180) REVERT: A 164 GLU cc_start: 0.8843 (pm20) cc_final: 0.8447 (pm20) REVERT: A 255 SER cc_start: 0.8989 (t) cc_final: 0.8744 (m) REVERT: A 288 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8321 (mp) REVERT: A 299 GLU cc_start: 0.8599 (mt-10) cc_final: 0.8313 (mt-10) REVERT: A 319 LEU cc_start: 0.8823 (mm) cc_final: 0.8136 (tp) REVERT: A 337 ASN cc_start: 0.8986 (t0) cc_final: 0.8745 (p0) REVERT: A 347 MET cc_start: 0.8522 (tmm) cc_final: 0.8239 (tmm) REVERT: A 677 LEU cc_start: 0.8111 (tm) cc_final: 0.7835 (pp) REVERT: A 688 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7172 (tm) REVERT: A 691 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: C 41 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8102 (mtm110) REVERT: C 164 GLU cc_start: 0.8830 (pm20) cc_final: 0.8424 (pm20) REVERT: C 255 SER cc_start: 0.8982 (t) cc_final: 0.8738 (m) REVERT: C 288 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8320 (mp) REVERT: C 299 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8376 (mt-10) REVERT: C 337 ASN cc_start: 0.8982 (t0) cc_final: 0.8671 (p0) REVERT: C 347 MET cc_start: 0.8537 (tmm) cc_final: 0.8197 (tmm) REVERT: C 677 LEU cc_start: 0.7843 (tm) cc_final: 0.7487 (pp) REVERT: C 688 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.7027 (tm) REVERT: C 691 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7469 (tt0) outliers start: 31 outliers final: 11 residues processed: 149 average time/residue: 0.4830 time to fit residues: 76.6480 Evaluate side-chains 133 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 511 ASP Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 0.6980 chunk 97 optimal weight: 0.0980 chunk 80 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 59 optimal weight: 0.3980 chunk 47 optimal weight: 0.0170 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.134401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.103249 restraints weight = 14510.939| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.52 r_work: 0.3373 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8092 Z= 0.138 Angle : 0.650 12.631 10996 Z= 0.309 Chirality : 0.041 0.204 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.404 27.808 1058 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.54 % Allowed : 15.47 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 2.30 (0.27), residues: 984 helix: 1.91 (0.18), residues: 804 sheet: None (None), residues: 0 loop : -0.14 (0.54), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 295 TYR 0.019 0.001 TYR C 451 PHE 0.029 0.002 PHE C 221 TRP 0.021 0.001 TRP A 679 HIS 0.003 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8092) covalent geometry : angle 0.64994 (10996) hydrogen bonds : bond 0.04541 ( 635) hydrogen bonds : angle 4.32700 ( 1881) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.227 Fit side-chains REVERT: A 164 GLU cc_start: 0.8875 (pm20) cc_final: 0.8407 (pm20) REVERT: A 255 SER cc_start: 0.8929 (t) cc_final: 0.8721 (m) REVERT: A 288 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8293 (mp) REVERT: A 299 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8340 (mt-10) REVERT: A 319 LEU cc_start: 0.8787 (mm) cc_final: 0.8067 (tp) REVERT: A 337 ASN cc_start: 0.8974 (t0) cc_final: 0.8762 (p0) REVERT: A 347 MET cc_start: 0.8537 (tmm) cc_final: 0.8247 (tmm) REVERT: A 385 ASP cc_start: 0.8153 (m-30) cc_final: 0.7858 (m-30) REVERT: A 677 LEU cc_start: 0.8086 (tm) cc_final: 0.7818 (pp) REVERT: A 688 LEU cc_start: 0.7175 (mm) cc_final: 0.6939 (tm) REVERT: A 691 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: C 41 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8021 (mtm110) REVERT: C 164 GLU cc_start: 0.8873 (pm20) cc_final: 0.8407 (pm20) REVERT: C 255 SER cc_start: 0.8930 (t) cc_final: 0.8728 (m) REVERT: C 288 LEU cc_start: 0.8531 (tp) cc_final: 0.8256 (mp) REVERT: C 299 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8388 (mt-10) REVERT: C 337 ASN cc_start: 0.8960 (t0) cc_final: 0.8706 (p0) REVERT: C 347 MET cc_start: 0.8533 (tmm) cc_final: 0.8172 (tmm) REVERT: C 677 LEU cc_start: 0.7771 (tm) cc_final: 0.7511 (pp) REVERT: C 688 LEU cc_start: 0.7460 (mm) cc_final: 0.7181 (tm) REVERT: C 691 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7504 (tt0) outliers start: 22 outliers final: 9 residues processed: 150 average time/residue: 0.4661 time to fit residues: 74.3352 Evaluate side-chains 136 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 377 TYR Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 4 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN C 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.131800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.100228 restraints weight = 14462.155| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.50 r_work: 0.3323 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8092 Z= 0.170 Angle : 0.652 13.059 10996 Z= 0.312 Chirality : 0.042 0.232 1310 Planarity : 0.004 0.033 1324 Dihedral : 4.423 25.686 1058 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.89 % Allowed : 15.82 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 2.06 (0.27), residues: 984 helix: 1.83 (0.18), residues: 818 sheet: None (None), residues: 0 loop : -0.95 (0.52), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 295 TYR 0.023 0.002 TYR C 451 PHE 0.028 0.002 PHE C 221 TRP 0.025 0.002 TRP A 679 HIS 0.002 0.001 HIS C 505 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 8092) covalent geometry : angle 0.65197 (10996) hydrogen bonds : bond 0.04782 ( 635) hydrogen bonds : angle 4.39781 ( 1881) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.252 Fit side-chains REVERT: A 41 ARG cc_start: 0.8419 (mtm180) cc_final: 0.8027 (mtm180) REVERT: A 146 ASP cc_start: 0.8877 (m-30) cc_final: 0.8470 (m-30) REVERT: A 164 GLU cc_start: 0.8926 (pm20) cc_final: 0.8551 (pm20) REVERT: A 255 SER cc_start: 0.9024 (t) cc_final: 0.8788 (m) REVERT: A 288 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8355 (mp) REVERT: A 299 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 319 LEU cc_start: 0.8849 (mm) cc_final: 0.8102 (tp) REVERT: A 341 GLU cc_start: 0.8650 (pm20) cc_final: 0.8364 (pm20) REVERT: A 347 MET cc_start: 0.8631 (tmm) cc_final: 0.8330 (tmm) REVERT: A 677 LEU cc_start: 0.8070 (tm) cc_final: 0.7846 (pp) REVERT: A 688 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6985 (tm) REVERT: A 691 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7717 (tt0) REVERT: C 41 ARG cc_start: 0.8392 (mtm-85) cc_final: 0.8018 (mtm110) REVERT: C 146 ASP cc_start: 0.8913 (m-30) cc_final: 0.8531 (m-30) REVERT: C 164 GLU cc_start: 0.8931 (pm20) cc_final: 0.8553 (pm20) REVERT: C 255 SER cc_start: 0.9028 (t) cc_final: 0.8794 (m) REVERT: C 288 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8353 (mp) REVERT: C 299 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8393 (mt-10) REVERT: C 337 ASN cc_start: 0.8981 (t0) cc_final: 0.8724 (p0) REVERT: C 341 GLU cc_start: 0.8672 (pm20) cc_final: 0.8398 (pm20) REVERT: C 347 MET cc_start: 0.8640 (tmm) cc_final: 0.8329 (tmm) REVERT: C 451 TYR cc_start: 0.7757 (m-80) cc_final: 0.7494 (m-80) REVERT: C 677 LEU cc_start: 0.7820 (tm) cc_final: 0.7586 (pp) REVERT: C 688 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7138 (tm) REVERT: C 691 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7503 (tt0) outliers start: 25 outliers final: 9 residues processed: 133 average time/residue: 0.5292 time to fit residues: 74.5843 Evaluate side-chains 132 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 27 optimal weight: 0.8980 chunk 43 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 82 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.102086 restraints weight = 14522.477| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.49 r_work: 0.3353 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8092 Z= 0.150 Angle : 0.632 12.121 10996 Z= 0.306 Chirality : 0.042 0.234 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.321 27.122 1058 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 3.12 % Allowed : 16.63 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 2.27 (0.27), residues: 984 helix: 1.94 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.77 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 295 TYR 0.021 0.002 TYR C 451 PHE 0.030 0.002 PHE C 221 TRP 0.027 0.002 TRP A 679 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8092) covalent geometry : angle 0.63248 (10996) hydrogen bonds : bond 0.04507 ( 635) hydrogen bonds : angle 4.34476 ( 1881) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.294 Fit side-chains REVERT: A 41 ARG cc_start: 0.8401 (mtm180) cc_final: 0.8003 (mtm180) REVERT: A 146 ASP cc_start: 0.8934 (m-30) cc_final: 0.8503 (m-30) REVERT: A 164 GLU cc_start: 0.8946 (pm20) cc_final: 0.8572 (pm20) REVERT: A 255 SER cc_start: 0.8987 (t) cc_final: 0.8747 (m) REVERT: A 288 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8330 (mp) REVERT: A 299 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8343 (mt-10) REVERT: A 319 LEU cc_start: 0.8824 (mm) cc_final: 0.8067 (tp) REVERT: A 341 GLU cc_start: 0.8698 (pm20) cc_final: 0.8445 (pm20) REVERT: A 347 MET cc_start: 0.8622 (tmm) cc_final: 0.8318 (tmm) REVERT: A 691 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7690 (tt0) REVERT: C 41 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.8041 (mtm110) REVERT: C 146 ASP cc_start: 0.8852 (m-30) cc_final: 0.8474 (m-30) REVERT: C 164 GLU cc_start: 0.8949 (pm20) cc_final: 0.8585 (pm20) REVERT: C 255 SER cc_start: 0.8985 (t) cc_final: 0.8750 (m) REVERT: C 288 LEU cc_start: 0.8647 (tp) cc_final: 0.8338 (mp) REVERT: C 299 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8400 (mt-10) REVERT: C 337 ASN cc_start: 0.8999 (t0) cc_final: 0.8779 (p0) REVERT: C 341 GLU cc_start: 0.8717 (pm20) cc_final: 0.8474 (pm20) REVERT: C 347 MET cc_start: 0.8637 (tmm) cc_final: 0.8323 (tmm) REVERT: C 385 ASP cc_start: 0.8195 (m-30) cc_final: 0.7893 (m-30) REVERT: C 688 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7137 (tm) REVERT: C 691 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7546 (tt0) outliers start: 27 outliers final: 6 residues processed: 134 average time/residue: 0.4736 time to fit residues: 67.6819 Evaluate side-chains 129 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 467 SER Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 70 optimal weight: 0.0060 chunk 51 optimal weight: 0.5980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.133394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.102207 restraints weight = 14558.147| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.50 r_work: 0.3357 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8092 Z= 0.149 Angle : 0.665 12.264 10996 Z= 0.312 Chirality : 0.042 0.293 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.307 26.507 1058 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.19 % Allowed : 16.86 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 2.25 (0.27), residues: 984 helix: 1.93 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.77 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 295 TYR 0.023 0.002 TYR C 689 PHE 0.027 0.002 PHE C 221 TRP 0.027 0.002 TRP A 679 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8092) covalent geometry : angle 0.66507 (10996) hydrogen bonds : bond 0.04490 ( 635) hydrogen bonds : angle 4.34002 ( 1881) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.324 Fit side-chains REVERT: A 41 ARG cc_start: 0.8420 (mtm180) cc_final: 0.8038 (mtm180) REVERT: A 146 ASP cc_start: 0.8930 (m-30) cc_final: 0.8527 (m-30) REVERT: A 164 GLU cc_start: 0.8956 (pm20) cc_final: 0.8581 (pm20) REVERT: A 255 SER cc_start: 0.9002 (t) cc_final: 0.8772 (m) REVERT: A 288 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8325 (mp) REVERT: A 299 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8342 (mt-10) REVERT: A 319 LEU cc_start: 0.8823 (mm) cc_final: 0.8554 (mm) REVERT: A 341 GLU cc_start: 0.8743 (pm20) cc_final: 0.8517 (pm20) REVERT: A 347 MET cc_start: 0.8624 (tmm) cc_final: 0.8316 (tmm) REVERT: A 447 PHE cc_start: 0.7292 (t80) cc_final: 0.7048 (t80) REVERT: A 691 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: C 41 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8021 (mtm110) REVERT: C 146 ASP cc_start: 0.8866 (m-30) cc_final: 0.8486 (m-30) REVERT: C 164 GLU cc_start: 0.8945 (pm20) cc_final: 0.8578 (pm20) REVERT: C 255 SER cc_start: 0.9004 (t) cc_final: 0.8779 (m) REVERT: C 288 LEU cc_start: 0.8639 (tp) cc_final: 0.8331 (mp) REVERT: C 299 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8401 (mt-10) REVERT: C 341 GLU cc_start: 0.8748 (pm20) cc_final: 0.8522 (pm20) REVERT: C 347 MET cc_start: 0.8639 (tmm) cc_final: 0.8325 (tmm) REVERT: C 688 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7151 (tm) REVERT: C 691 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7416 (tt0) REVERT: C 695 PHE cc_start: 0.8350 (m-80) cc_final: 0.8104 (m-80) outliers start: 19 outliers final: 7 residues processed: 135 average time/residue: 0.4978 time to fit residues: 71.5182 Evaluate side-chains 131 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 10 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 59 optimal weight: 0.5980 chunk 16 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3950 r_free = 0.3950 target = 0.133826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.102438 restraints weight = 14421.918| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.48 r_work: 0.3363 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8092 Z= 0.152 Angle : 0.670 12.454 10996 Z= 0.320 Chirality : 0.043 0.317 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.285 26.376 1058 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.08 % Allowed : 17.09 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 2.33 (0.27), residues: 984 helix: 1.99 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.76 (0.54), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 295 TYR 0.022 0.002 TYR C 689 PHE 0.029 0.001 PHE C 221 TRP 0.029 0.002 TRP A 679 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 8092) covalent geometry : angle 0.66985 (10996) hydrogen bonds : bond 0.04467 ( 635) hydrogen bonds : angle 4.31319 ( 1881) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.263 Fit side-chains REVERT: A 41 ARG cc_start: 0.8424 (mtm180) cc_final: 0.8039 (mtm180) REVERT: A 146 ASP cc_start: 0.8908 (m-30) cc_final: 0.8573 (m-30) REVERT: A 164 GLU cc_start: 0.8943 (pm20) cc_final: 0.8580 (pm20) REVERT: A 255 SER cc_start: 0.9004 (t) cc_final: 0.8780 (m) REVERT: A 288 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8327 (mp) REVERT: A 299 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8361 (mt-10) REVERT: A 319 LEU cc_start: 0.8817 (mm) cc_final: 0.8549 (mm) REVERT: A 341 GLU cc_start: 0.8699 (pm20) cc_final: 0.8468 (pm20) REVERT: A 347 MET cc_start: 0.8632 (tmm) cc_final: 0.8324 (tmm) REVERT: A 691 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7652 (tt0) REVERT: C 41 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.8024 (mtm110) REVERT: C 146 ASP cc_start: 0.8851 (m-30) cc_final: 0.8465 (m-30) REVERT: C 164 GLU cc_start: 0.8948 (pm20) cc_final: 0.8580 (pm20) REVERT: C 288 LEU cc_start: 0.8636 (tp) cc_final: 0.8331 (mp) REVERT: C 299 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8386 (mt-10) REVERT: C 341 GLU cc_start: 0.8720 (pm20) cc_final: 0.8476 (pm20) REVERT: C 347 MET cc_start: 0.8652 (tmm) cc_final: 0.8331 (tmm) REVERT: C 688 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7152 (tm) REVERT: C 691 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: C 695 PHE cc_start: 0.8333 (m-80) cc_final: 0.8098 (m-80) outliers start: 18 outliers final: 8 residues processed: 131 average time/residue: 0.5197 time to fit residues: 72.3216 Evaluate side-chains 131 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 401 LEU Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 688 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 35 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.133753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.102216 restraints weight = 14418.868| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.49 r_work: 0.3357 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8092 Z= 0.154 Angle : 0.681 12.573 10996 Z= 0.323 Chirality : 0.043 0.321 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.265 26.075 1058 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.96 % Allowed : 17.32 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 2.28 (0.27), residues: 984 helix: 1.96 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.90 (0.53), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 295 TYR 0.020 0.002 TYR C 451 PHE 0.027 0.002 PHE A 447 TRP 0.034 0.002 TRP C 432 HIS 0.002 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 8092) covalent geometry : angle 0.68075 (10996) hydrogen bonds : bond 0.04472 ( 635) hydrogen bonds : angle 4.30944 ( 1881) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.302 Fit side-chains REVERT: A 41 ARG cc_start: 0.8413 (mtm180) cc_final: 0.8015 (mtm180) REVERT: A 146 ASP cc_start: 0.8896 (m-30) cc_final: 0.8695 (m-30) REVERT: A 164 GLU cc_start: 0.8952 (pm20) cc_final: 0.8591 (pm20) REVERT: A 255 SER cc_start: 0.9008 (t) cc_final: 0.8794 (m) REVERT: A 288 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8333 (mp) REVERT: A 299 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8349 (mt-10) REVERT: A 319 LEU cc_start: 0.8821 (mm) cc_final: 0.8554 (mm) REVERT: A 341 GLU cc_start: 0.8721 (pm20) cc_final: 0.8477 (pm20) REVERT: A 347 MET cc_start: 0.8631 (tmm) cc_final: 0.8315 (tmm) REVERT: A 691 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: C 41 ARG cc_start: 0.8399 (mtm-85) cc_final: 0.8030 (mtm110) REVERT: C 146 ASP cc_start: 0.8860 (m-30) cc_final: 0.8475 (m-30) REVERT: C 164 GLU cc_start: 0.8952 (pm20) cc_final: 0.8584 (pm20) REVERT: C 288 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8332 (mp) REVERT: C 299 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8412 (mt-10) REVERT: C 341 GLU cc_start: 0.8713 (pm20) cc_final: 0.8489 (pm20) REVERT: C 347 MET cc_start: 0.8647 (tmm) cc_final: 0.8322 (tmm) REVERT: C 691 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7497 (tt0) REVERT: C 695 PHE cc_start: 0.8340 (m-80) cc_final: 0.8068 (m-80) outliers start: 17 outliers final: 8 residues processed: 128 average time/residue: 0.5397 time to fit residues: 73.2776 Evaluate side-chains 131 residues out of total 874 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 240 TYR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 240 TYR Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 691 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 58 optimal weight: 0.0870 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 0.0370 chunk 38 optimal weight: 0.7980 chunk 77 optimal weight: 0.0470 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 87 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.1734 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.138096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.107238 restraints weight = 14345.189| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.49 r_work: 0.3442 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8092 Z= 0.130 Angle : 0.673 12.568 10996 Z= 0.316 Chirality : 0.042 0.303 1310 Planarity : 0.004 0.034 1324 Dihedral : 4.139 26.402 1058 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.15 % Allowed : 18.48 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 aren not related in a simple way. whole: 2.54 (0.28), residues: 984 helix: 2.13 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.76 (0.55), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 295 TYR 0.019 0.001 TYR C 451 PHE 0.029 0.001 PHE C 221 TRP 0.039 0.002 TRP C 432 HIS 0.002 0.000 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8092) covalent geometry : angle 0.67285 (10996) hydrogen bonds : bond 0.04065 ( 635) hydrogen bonds : angle 4.15587 ( 1881) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2955.94 seconds wall clock time: 51 minutes 4.44 seconds (3064.44 seconds total)