Starting phenix.real_space_refine on Sat Dec 28 06:19:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sp6_25366/12_2024/7sp6_25366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sp6_25366/12_2024/7sp6_25366.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7sp6_25366/12_2024/7sp6_25366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sp6_25366/12_2024/7sp6_25366.map" model { file = "/net/cci-nas-00/data/ceres_data/7sp6_25366/12_2024/7sp6_25366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sp6_25366/12_2024/7sp6_25366.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1808 atoms to isotropic. 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 Mn 1 7.51 5 P 1 5.49 5 S 35 5.16 5 C 3858 2.51 5 N 977 2.21 5 O 1085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5957 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 4013 Classifications: {'peptide': 493} Link IDs: {'PTRANS': 13, 'TRANS': 479} Chain breaks: 1 Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "C" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 916 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain breaks: 1 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' MN': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.07, per 1000 atoms: 0.68 Number of scatterers: 5957 At special positions: 0 Unit cell: (72.36, 76.68, 155.52, 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) Mn 1 24.99 S 35 16.00 P 1 15.00 O 1085 8.00 N 977 7.00 C 3858 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 2.32 Conformation dependent library (CDL) restraints added in 879.3 milliseconds 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1358 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 7 sheets defined 46.8% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 38 through 74 removed outlier: 3.646A pdb=" N LEU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 108 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.946A pdb=" N ALA A 131 " --> pdb=" O ASP A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.539A pdb=" N ILE A 160 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 3.594A pdb=" N SER A 180 " --> pdb=" O GLY A 176 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 221 Proline residue: A 217 - end of helix removed outlier: 3.683A pdb=" N CYS A 220 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.938A pdb=" N ARG A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY A 257 " --> pdb=" O ASN A 253 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 290 removed outlier: 5.236A pdb=" N ASP A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 286 - end of helix removed outlier: 3.621A pdb=" N GLN A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 removed outlier: 3.967A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 360 removed outlier: 4.485A pdb=" N TRP A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N TYR A 352 " --> pdb=" O ARG A 348 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY A 355 " --> pdb=" O TRP A 351 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 392 removed outlier: 3.757A pdb=" N ILE A 375 " --> pdb=" O CYS A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 420 Processing helix chain 'A' and resid 421 through 428 removed outlier: 3.808A pdb=" N ALA A 424 " --> pdb=" O ASN A 421 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 425 " --> pdb=" O LEU A 422 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 449 removed outlier: 3.878A pdb=" N VAL A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE A 439 " --> pdb=" O PHE A 435 " (cutoff:3.500A) Proline residue: A 440 - end of helix Processing helix chain 'A' and resid 476 through 497 Processing helix chain 'A' and resid 504 through 535 removed outlier: 3.590A pdb=" N ILE A 533 " --> pdb=" O LEU A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 551 removed outlier: 3.566A pdb=" N LYS A 543 " --> pdb=" O THR A 539 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.704A pdb=" N TYR B 111 " --> pdb=" O THR B 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 169 through 171 removed outlier: 8.089A pdb=" N ILE A 170 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N CYS A 118 " --> pdb=" O ILE A 170 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL A 84 " --> pdb=" O ARG A 115 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N ILE A 117 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N VAL A 86 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A 119 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE A 88 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 89 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 227 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N LYS A 225 " --> pdb=" O THR A 276 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE A 224 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N TYR A 318 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 10.478A pdb=" N ALA A 226 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 10.227A pdb=" N ALA A 228 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA A 322 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.387A pdb=" N PHE A 500 " --> pdb=" O GLY B 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 3 through 8 removed outlier: 3.974A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N THR B 68 " --> pdb=" O GLN B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 11 through 12 removed outlier: 7.457A pdb=" N THR B 121 " --> pdb=" O VAL B 12 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 5.825A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.767A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER C 7 " --> pdb=" O ALA C 21 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 18 " --> pdb=" O MET C 82 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU C 81 " --> pdb=" O THR C 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 59 removed outlier: 4.336A pdb=" N ALA C 49 " --> pdb=" O TRP C 36 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 34 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR C 33 " --> pdb=" O ARG C 98 " (cutoff:3.500A) 287 hydrogen bonds defined for protein. 822 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: 1.83 Time building geometry restraints manager: 2.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1024 1.33 - 1.45: 1741 1.45 - 1.57: 3268 1.57 - 1.69: 18 1.69 - 1.82: 53 Bond restraints: 6104 Sorted by residual: bond pdb=" CBD Y01 A 601 " pdb=" CBG Y01 A 601 " ideal model delta sigma weight residual 1.520 1.643 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" CAV Y01 A 601 " pdb=" CAZ Y01 A 601 " ideal model delta sigma weight residual 1.507 1.609 -0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 1.332 1.425 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" CAV Y01 A 601 " pdb=" CBC Y01 A 601 " ideal model delta sigma weight residual 1.523 1.613 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" CBF Y01 A 601 " pdb=" CBH Y01 A 601 " ideal model delta sigma weight residual 1.550 1.639 -0.089 2.00e-02 2.50e+03 1.97e+01 ... (remaining 6099 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 8207 2.63 - 5.25: 46 5.25 - 7.88: 16 7.88 - 10.51: 2 10.51 - 13.14: 3 Bond angle restraints: 8274 Sorted by residual: angle pdb=" CAM Y01 A 601 " pdb=" CAY Y01 A 601 " pdb=" OAW Y01 A 601 " ideal model delta sigma weight residual 111.19 124.33 -13.14 3.00e+00 1.11e-01 1.92e+01 angle pdb=" CAI Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CAV Y01 A 601 " ideal model delta sigma weight residual 120.03 131.73 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" CAZ Y01 A 601 " pdb=" CAV Y01 A 601 " pdb=" CBC Y01 A 601 " ideal model delta sigma weight residual 111.19 122.29 -11.10 3.00e+00 1.11e-01 1.37e+01 angle pdb=" C ASN A 253 " pdb=" N VAL A 254 " pdb=" CA VAL A 254 " ideal model delta sigma weight residual 122.97 120.27 2.70 9.80e-01 1.04e+00 7.60e+00 angle pdb=" CAV Y01 A 601 " pdb=" CAZ Y01 A 601 " pdb=" CBH Y01 A 601 " ideal model delta sigma weight residual 116.96 108.83 8.13 3.00e+00 1.11e-01 7.34e+00 ... (remaining 8269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3265 17.95 - 35.89: 266 35.89 - 53.84: 63 53.84 - 71.78: 13 71.78 - 89.73: 7 Dihedral angle restraints: 3614 sinusoidal: 1479 harmonic: 2135 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 55.78 37.22 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA ASP A 77 " pdb=" CB ASP A 77 " pdb=" CG ASP A 77 " pdb=" OD1 ASP A 77 " ideal model delta sinusoidal sigma weight residual -30.00 -87.74 57.74 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA ASP A 121 " pdb=" CB ASP A 121 " pdb=" CG ASP A 121 " pdb=" OD1 ASP A 121 " ideal model delta sinusoidal sigma weight residual -30.00 -83.41 53.41 1 2.00e+01 2.50e-03 9.69e+00 ... (remaining 3611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 837 0.080 - 0.159: 56 0.159 - 0.239: 1 0.239 - 0.318: 1 0.318 - 0.398: 3 Chirality restraints: 898 Sorted by residual: chirality pdb=" CBG Y01 A 601 " pdb=" CAQ Y01 A 601 " pdb=" CBD Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CBE Y01 A 601 " pdb=" CAP Y01 A 601 " pdb=" CBB Y01 A 601 " pdb=" CBI Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.57 2.93 -0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CBI Y01 A 601 " pdb=" CAU Y01 A 601 " pdb=" CBE Y01 A 601 " pdb=" CBG Y01 A 601 " both_signs ideal model delta sigma weight residual False 2.94 2.61 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 895 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 319 " -0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 320 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 144 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.25e-01 pdb=" N PRO A 145 " -0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 145 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 145 " 0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 76 " 0.004 2.00e-02 2.50e+03 7.24e-03 5.24e-01 pdb=" C ASN C 76 " -0.013 2.00e-02 2.50e+03 pdb=" O ASN C 76 " 0.005 2.00e-02 2.50e+03 pdb=" N THR C 77 " 0.004 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1826 2.83 - 3.34: 5483 3.34 - 3.86: 9524 3.86 - 4.38: 10524 4.38 - 4.90: 18554 Nonbonded interactions: 45911 Sorted by model distance: nonbonded pdb=" O TRP A 234 " pdb=" OG1 THR A 539 " model vdw 2.308 3.040 nonbonded pdb=" O TYR A 499 " pdb=" OH TYR A 507 " model vdw 2.355 3.040 nonbonded pdb=" OG SER C 51 " pdb=" O GLY C 56 " model vdw 2.358 3.040 nonbonded pdb=" ND2 ASN A 139 " pdb=" O LYS A 166 " model vdw 2.377 3.120 nonbonded pdb=" OE1 GLN A 172 " pdb=" OG1 THR A 183 " model vdw 2.379 3.040 ... (remaining 45906 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.090 Process input model: 18.660 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.123 6104 Z= 0.294 Angle : 0.577 13.136 8274 Z= 0.253 Chirality : 0.045 0.398 898 Planarity : 0.002 0.031 1020 Dihedral : 14.433 89.727 2250 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.31), residues: 723 helix: 2.49 (0.30), residues: 302 sheet: 1.88 (0.45), residues: 135 loop : -0.78 (0.33), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 53 HIS 0.000 0.000 HIS A 360 PHE 0.005 0.001 PHE C 37 TYR 0.011 0.001 TYR A 480 ARG 0.001 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.703 Fit side-chains REVERT: B 55 GLU cc_start: 0.8646 (mp0) cc_final: 0.8337 (mp0) REVERT: B 88 GLU cc_start: 0.7635 (pp20) cc_final: 0.7424 (mp0) REVERT: C 3 GLN cc_start: 0.8374 (mp-120) cc_final: 0.8172 (mm-40) REVERT: C 85 LEU cc_start: 0.8997 (mp) cc_final: 0.8758 (mp) REVERT: C 103 SER cc_start: 0.7719 (t) cc_final: 0.6861 (t) REVERT: C 118 GLN cc_start: 0.7834 (tp40) cc_final: 0.7564 (mm-40) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1633 time to fit residues: 26.2739 Evaluate side-chains 96 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6104 Z= 0.215 Angle : 0.513 5.522 8274 Z= 0.271 Chirality : 0.041 0.156 898 Planarity : 0.003 0.026 1020 Dihedral : 6.013 56.905 939 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.96 % Allowed : 8.81 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.31), residues: 723 helix: 2.48 (0.29), residues: 312 sheet: 1.46 (0.44), residues: 132 loop : -1.15 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.002 0.001 HIS A 174 PHE 0.018 0.002 PHE A 185 TYR 0.019 0.001 TYR A 46 ARG 0.002 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 106 time to evaluate : 0.631 Fit side-chains REVERT: B 55 GLU cc_start: 0.8679 (mp0) cc_final: 0.8285 (mp0) REVERT: B 59 TYR cc_start: 0.8787 (m-80) cc_final: 0.8397 (m-10) REVERT: C 3 GLN cc_start: 0.8400 (mp-120) cc_final: 0.8170 (mm-40) REVERT: C 115 TYR cc_start: 0.7998 (m-10) cc_final: 0.7745 (m-10) REVERT: C 118 GLN cc_start: 0.7971 (tp40) cc_final: 0.7660 (mm-40) outliers start: 6 outliers final: 4 residues processed: 110 average time/residue: 0.1449 time to fit residues: 22.2450 Evaluate side-chains 92 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 542 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6104 Z= 0.298 Angle : 0.571 6.789 8274 Z= 0.309 Chirality : 0.043 0.167 898 Planarity : 0.003 0.024 1020 Dihedral : 6.454 50.869 939 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.56 % Allowed : 14.42 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.30), residues: 723 helix: 2.16 (0.29), residues: 312 sheet: 0.99 (0.42), residues: 140 loop : -1.34 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 246 HIS 0.002 0.001 HIS A 174 PHE 0.018 0.002 PHE A 185 TYR 0.022 0.002 TYR C 105 ARG 0.003 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.725 Fit side-chains REVERT: B 3 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8079 (mm110) REVERT: B 30 LYS cc_start: 0.8325 (pttm) cc_final: 0.8099 (ptmt) REVERT: B 55 GLU cc_start: 0.8739 (mp0) cc_final: 0.8410 (mp0) REVERT: C 2 VAL cc_start: 0.7507 (t) cc_final: 0.7287 (t) REVERT: C 3 GLN cc_start: 0.8400 (mp-120) cc_final: 0.8077 (mm-40) outliers start: 16 outliers final: 10 residues processed: 112 average time/residue: 0.1927 time to fit residues: 28.0216 Evaluate side-chains 102 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6104 Z= 0.260 Angle : 0.532 6.074 8274 Z= 0.288 Chirality : 0.042 0.162 898 Planarity : 0.003 0.026 1020 Dihedral : 6.164 44.497 939 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.37 % Allowed : 15.87 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 723 helix: 2.15 (0.29), residues: 312 sheet: 0.87 (0.42), residues: 139 loop : -1.44 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.002 0.001 HIS A 174 PHE 0.013 0.001 PHE A 520 TYR 0.015 0.002 TYR C 105 ARG 0.006 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 94 time to evaluate : 0.713 Fit side-chains REVERT: B 30 LYS cc_start: 0.8411 (pttm) cc_final: 0.8166 (ptmt) REVERT: B 55 GLU cc_start: 0.8736 (mp0) cc_final: 0.8405 (mp0) REVERT: C 3 GLN cc_start: 0.8365 (mp-120) cc_final: 0.7993 (mm-40) outliers start: 21 outliers final: 15 residues processed: 105 average time/residue: 0.2029 time to fit residues: 27.3928 Evaluate side-chains 103 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6104 Z= 0.232 Angle : 0.516 6.854 8274 Z= 0.279 Chirality : 0.041 0.160 898 Planarity : 0.003 0.033 1020 Dihedral : 6.055 43.703 939 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.04 % Allowed : 15.71 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.30), residues: 723 helix: 2.20 (0.29), residues: 312 sheet: 0.59 (0.42), residues: 142 loop : -1.40 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 PHE 0.013 0.001 PHE A 520 TYR 0.012 0.001 TYR A 414 ARG 0.006 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.759 Fit side-chains REVERT: A 311 MET cc_start: 0.6479 (mmt) cc_final: 0.6235 (mtt) REVERT: B 30 LYS cc_start: 0.8522 (pttm) cc_final: 0.8254 (ptmm) REVERT: B 55 GLU cc_start: 0.8770 (mp0) cc_final: 0.8330 (mp0) REVERT: C 3 GLN cc_start: 0.8369 (mp-120) cc_final: 0.7886 (mm-40) outliers start: 19 outliers final: 13 residues processed: 103 average time/residue: 0.1884 time to fit residues: 25.8596 Evaluate side-chains 105 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 0.9980 chunk 62 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6104 Z= 0.403 Angle : 0.623 7.888 8274 Z= 0.339 Chirality : 0.045 0.168 898 Planarity : 0.004 0.030 1020 Dihedral : 6.761 46.133 939 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.49 % Allowed : 16.51 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.30), residues: 723 helix: 1.96 (0.29), residues: 312 sheet: 0.29 (0.42), residues: 145 loop : -1.59 (0.33), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 246 HIS 0.002 0.001 HIS A 174 PHE 0.017 0.002 PHE A 476 TYR 0.021 0.002 TYR C 105 ARG 0.006 0.001 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.658 Fit side-chains REVERT: A 311 MET cc_start: 0.6341 (mmt) cc_final: 0.5925 (mtt) REVERT: B 30 LYS cc_start: 0.8751 (pttm) cc_final: 0.8431 (ptmt) REVERT: B 46 GLU cc_start: 0.8401 (pt0) cc_final: 0.8153 (pt0) REVERT: B 55 GLU cc_start: 0.8765 (mp0) cc_final: 0.8425 (mp0) REVERT: C 3 GLN cc_start: 0.8285 (mp-120) cc_final: 0.7680 (mm-40) outliers start: 28 outliers final: 20 residues processed: 110 average time/residue: 0.1773 time to fit residues: 26.4660 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 HIS Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 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 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6104 Z= 0.193 Angle : 0.535 7.899 8274 Z= 0.286 Chirality : 0.041 0.154 898 Planarity : 0.003 0.026 1020 Dihedral : 6.449 49.760 939 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.21 % Allowed : 18.43 % Favored : 78.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.30), residues: 723 helix: 2.18 (0.28), residues: 312 sheet: 0.36 (0.40), residues: 153 loop : -1.64 (0.33), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.001 0.001 HIS A 360 PHE 0.031 0.001 PHE A 49 TYR 0.012 0.001 TYR A 414 ARG 0.005 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.670 Fit side-chains REVERT: A 311 MET cc_start: 0.6539 (mmt) cc_final: 0.6173 (mtt) REVERT: A 333 MET cc_start: 0.8334 (mmm) cc_final: 0.7320 (mmm) REVERT: B 30 LYS cc_start: 0.8725 (pttm) cc_final: 0.8428 (ptmm) REVERT: B 55 GLU cc_start: 0.8769 (mp0) cc_final: 0.8330 (mp0) REVERT: C 3 GLN cc_start: 0.8304 (mp-120) cc_final: 0.7706 (mm110) outliers start: 20 outliers final: 15 residues processed: 109 average time/residue: 0.1726 time to fit residues: 25.1002 Evaluate side-chains 106 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 0.7980 chunk 13 optimal weight: 0.0870 chunk 44 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.4954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6104 Z= 0.180 Angle : 0.535 7.951 8274 Z= 0.285 Chirality : 0.041 0.234 898 Planarity : 0.003 0.025 1020 Dihedral : 6.312 49.171 939 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.53 % Allowed : 19.23 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.31), residues: 723 helix: 2.31 (0.29), residues: 312 sheet: 0.34 (0.40), residues: 153 loop : -1.57 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 53 HIS 0.001 0.000 HIS A 360 PHE 0.029 0.001 PHE A 49 TYR 0.020 0.001 TYR C 105 ARG 0.005 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.643 Fit side-chains REVERT: A 311 MET cc_start: 0.6523 (mmt) cc_final: 0.6165 (mtt) REVERT: A 333 MET cc_start: 0.8222 (mmm) cc_final: 0.7313 (mmm) REVERT: A 481 MET cc_start: 0.8245 (mtp) cc_final: 0.7921 (mtp) REVERT: B 30 LYS cc_start: 0.8714 (pttm) cc_final: 0.8419 (ptmm) REVERT: B 55 GLU cc_start: 0.8770 (mp0) cc_final: 0.8327 (mp0) REVERT: C 3 GLN cc_start: 0.8296 (mp-120) cc_final: 0.7700 (mm110) outliers start: 22 outliers final: 19 residues processed: 108 average time/residue: 0.1716 time to fit residues: 24.8142 Evaluate side-chains 110 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 50 optimal weight: 0.0870 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6104 Z= 0.166 Angle : 0.530 8.334 8274 Z= 0.278 Chirality : 0.041 0.213 898 Planarity : 0.003 0.026 1020 Dihedral : 6.172 47.108 939 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.21 % Allowed : 19.55 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.31), residues: 723 helix: 2.37 (0.29), residues: 312 sheet: 0.32 (0.40), residues: 153 loop : -1.54 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 53 HIS 0.001 0.000 HIS A 360 PHE 0.027 0.001 PHE A 49 TYR 0.019 0.001 TYR C 105 ARG 0.005 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.677 Fit side-chains REVERT: A 311 MET cc_start: 0.6551 (mmt) cc_final: 0.6234 (mtt) REVERT: A 333 MET cc_start: 0.8238 (mmm) cc_final: 0.7286 (mmm) REVERT: A 481 MET cc_start: 0.8299 (mtp) cc_final: 0.8020 (mtp) REVERT: B 30 LYS cc_start: 0.8697 (pttm) cc_final: 0.8413 (ptmm) REVERT: B 55 GLU cc_start: 0.8760 (mp0) cc_final: 0.8320 (mp0) REVERT: C 3 GLN cc_start: 0.8289 (mp-120) cc_final: 0.7690 (mm110) outliers start: 20 outliers final: 19 residues processed: 110 average time/residue: 0.1731 time to fit residues: 25.3638 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 60 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6104 Z= 0.164 Angle : 0.519 8.604 8274 Z= 0.275 Chirality : 0.040 0.208 898 Planarity : 0.003 0.029 1020 Dihedral : 6.041 43.541 939 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.37 % Allowed : 19.87 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.31), residues: 723 helix: 2.42 (0.29), residues: 312 sheet: 0.31 (0.40), residues: 150 loop : -1.56 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 PHE 0.025 0.001 PHE A 49 TYR 0.017 0.001 TYR A 373 ARG 0.007 0.000 ARG B 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1446 Ramachandran restraints generated. 723 Oldfield, 0 Emsley, 723 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 0.686 Fit side-chains REVERT: A 311 MET cc_start: 0.6654 (mmt) cc_final: 0.6211 (mtt) REVERT: A 333 MET cc_start: 0.8223 (mmm) cc_final: 0.7291 (mmm) REVERT: B 30 LYS cc_start: 0.8705 (pttm) cc_final: 0.8426 (ptmm) REVERT: B 55 GLU cc_start: 0.8763 (mp0) cc_final: 0.8330 (mp0) REVERT: C 3 GLN cc_start: 0.8325 (mp-120) cc_final: 0.7714 (mm110) outliers start: 21 outliers final: 18 residues processed: 108 average time/residue: 0.1825 time to fit residues: 26.1350 Evaluate side-chains 109 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 358 TRP Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 GLU Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 41 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN B 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.111088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093957 restraints weight = 10000.067| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.59 r_work: 0.3113 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6104 Z= 0.159 Angle : 0.529 8.560 8274 Z= 0.276 Chirality : 0.040 0.198 898 Planarity : 0.003 0.032 1020 Dihedral : 6.003 42.017 939 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.04 % Allowed : 19.71 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.31), residues: 723 helix: 2.42 (0.29), residues: 312 sheet: 0.33 (0.40), residues: 150 loop : -1.52 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 PHE 0.025 0.001 PHE A 49 TYR 0.018 0.001 TYR C 105 ARG 0.007 0.000 ARG B 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1551.33 seconds wall clock time: 28 minutes 55.72 seconds (1735.72 seconds total)