Starting phenix.real_space_refine on Tue Mar 3 18:19:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sp6_25366/03_2026/7sp6_25366.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sp6_25366/03_2026/7sp6_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 { model { file = "/net/cci-nas-00/data/ceres_data/7sp6_25366/03_2026/7sp6_25366.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sp6_25366/03_2026/7sp6_25366.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sp6_25366/03_2026/7sp6_25366.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sp6_25366/03_2026/7sp6_25366.map" } resolution = 3.1 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= 0.032 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.27, per 1000 atoms: 0.21 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: 0.46 Conformation dependent library (CDL) restraints added in 152.8 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: 0.19 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: 0.87 Time building geometry restraints manager: 0.61 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.390 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.910 ------------------------------------------------------------------------------- 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 6106 Z= 0.221 Angle : 0.577 13.136 8278 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (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 ARG 0.001 0.000 ARG B 66 TYR 0.011 0.001 TYR A 480 PHE 0.005 0.001 PHE C 37 TRP 0.004 0.000 TRP C 53 HIS 0.000 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 6104) covalent geometry : angle 0.57670 ( 8274) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.25741 ( 4) hydrogen bonds : bond 0.18098 ( 287) hydrogen bonds : angle 5.69737 ( 822) *********************** 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 : 0.149 Fit side-chains REVERT: B 55 GLU cc_start: 0.8646 (mp0) cc_final: 0.8338 (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: 0.7835 (tp40) cc_final: 0.7564 (mm-40) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0645 time to fit residues: 10.5748 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 : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.0070 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7202 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.130456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.111998 restraints weight = 10041.826| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 2.81 r_work: 0.3385 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6106 Z= 0.125 Angle : 0.514 5.455 8278 Z= 0.267 Chirality : 0.040 0.155 898 Planarity : 0.003 0.026 1020 Dihedral : 6.032 57.692 939 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.80 % Allowed : 9.29 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.31), residues: 723 helix: 2.46 (0.29), residues: 312 sheet: 1.42 (0.44), residues: 132 loop : -1.13 (0.33), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 178 TYR 0.020 0.001 TYR A 46 PHE 0.020 0.001 PHE A 185 TRP 0.009 0.001 TRP C 53 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 6104) covalent geometry : angle 0.51359 ( 8274) SS BOND : bond 0.00367 ( 2) SS BOND : angle 0.62085 ( 4) hydrogen bonds : bond 0.03495 ( 287) hydrogen bonds : angle 3.97485 ( 822) *********************** 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 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 111 time to evaluate : 0.247 Fit side-chains REVERT: A 426 TYR cc_start: 0.6910 (m-10) cc_final: 0.6624 (m-10) REVERT: B 3 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7554 (mm-40) REVERT: B 55 GLU cc_start: 0.9023 (mp0) cc_final: 0.8642 (mp0) REVERT: B 59 TYR cc_start: 0.8840 (m-80) cc_final: 0.8402 (m-10) REVERT: C 3 GLN cc_start: 0.8436 (mp-120) cc_final: 0.8191 (mm-40) REVERT: C 115 TYR cc_start: 0.8094 (m-10) cc_final: 0.7843 (m-10) REVERT: C 118 GLN cc_start: 0.8232 (tp40) cc_final: 0.7899 (mm-40) outliers start: 5 outliers final: 2 residues processed: 115 average time/residue: 0.0592 time to fit residues: 9.7275 Evaluate side-chains 95 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 33 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.0870 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9962 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.117432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099373 restraints weight = 10058.664| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.69 r_work: 0.3209 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6106 Z= 0.145 Angle : 0.514 5.358 8278 Z= 0.274 Chirality : 0.041 0.165 898 Planarity : 0.003 0.023 1020 Dihedral : 6.128 48.854 939 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.24 % Allowed : 14.10 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.31), residues: 723 helix: 2.33 (0.29), residues: 312 sheet: 1.08 (0.41), residues: 140 loop : -1.21 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 92 TYR 0.018 0.002 TYR A 550 PHE 0.014 0.002 PHE A 520 TRP 0.009 0.001 TRP A 246 HIS 0.002 0.001 HIS A 552 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 6104) covalent geometry : angle 0.51443 ( 8274) SS BOND : bond 0.00342 ( 2) SS BOND : angle 0.42374 ( 4) hydrogen bonds : bond 0.04144 ( 287) hydrogen bonds : angle 3.73203 ( 822) *********************** 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: 14 poor density : 103 time to evaluate : 0.155 Fit side-chains REVERT: A 426 TYR cc_start: 0.7776 (m-10) cc_final: 0.7458 (m-10) REVERT: B 55 GLU cc_start: 0.9001 (mp0) cc_final: 0.8579 (mp0) REVERT: C 2 VAL cc_start: 0.7494 (t) cc_final: 0.7233 (t) REVERT: C 3 GLN cc_start: 0.8549 (mp-120) cc_final: 0.8207 (mm-40) outliers start: 14 outliers final: 9 residues processed: 110 average time/residue: 0.0793 time to fit residues: 11.5103 Evaluate side-chains 101 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 92 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 48 VAL Chi-restraints excluded: chain C residue 4 LEU 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 54 optimal weight: 0.6980 chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.0980 chunk 71 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3592 r_free = 0.3592 target = 0.118297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.100457 restraints weight = 10051.739| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.69 r_work: 0.3219 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6106 Z= 0.105 Angle : 0.484 10.340 8278 Z= 0.254 Chirality : 0.040 0.182 898 Planarity : 0.003 0.024 1020 Dihedral : 5.645 45.981 939 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.60 % Allowed : 17.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.31), residues: 723 helix: 2.40 (0.29), residues: 312 sheet: 0.98 (0.41), residues: 140 loop : -1.24 (0.34), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 27 TYR 0.014 0.001 TYR A 366 PHE 0.010 0.001 PHE A 520 TRP 0.009 0.001 TRP C 53 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 6104) covalent geometry : angle 0.48435 ( 8274) SS BOND : bond 0.00316 ( 2) SS BOND : angle 0.45465 ( 4) hydrogen bonds : bond 0.03397 ( 287) hydrogen bonds : angle 3.57567 ( 822) *********************** 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 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.233 Fit side-chains REVERT: A 178 ARG cc_start: 0.7604 (mtp85) cc_final: 0.7365 (mmm-85) REVERT: A 426 TYR cc_start: 0.7745 (m-10) cc_final: 0.7394 (m-10) REVERT: B 30 LYS cc_start: 0.8247 (pttm) cc_final: 0.7845 (ptmt) REVERT: B 55 GLU cc_start: 0.9045 (mp0) cc_final: 0.8630 (mp0) REVERT: B 59 TYR cc_start: 0.8994 (m-80) cc_final: 0.8467 (m-80) REVERT: C 2 VAL cc_start: 0.7537 (t) cc_final: 0.7296 (t) REVERT: C 3 GLN cc_start: 0.8514 (mp-120) cc_final: 0.8163 (mm-40) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 0.0845 time to fit residues: 12.0409 Evaluate side-chains 101 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 96 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain C residue 25 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 29 optimal weight: 0.0010 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 542 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.116241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.098499 restraints weight = 10153.644| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.68 r_work: 0.3183 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6106 Z= 0.113 Angle : 0.486 6.984 8278 Z= 0.258 Chirality : 0.041 0.205 898 Planarity : 0.003 0.028 1020 Dihedral : 5.586 39.073 939 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.88 % Allowed : 15.87 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.31), residues: 723 helix: 2.42 (0.29), residues: 312 sheet: 0.79 (0.42), residues: 139 loop : -1.26 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.017 0.001 TYR C 105 PHE 0.010 0.001 PHE C 47 TRP 0.008 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6104) covalent geometry : angle 0.48605 ( 8274) SS BOND : bond 0.00323 ( 2) SS BOND : angle 0.40701 ( 4) hydrogen bonds : bond 0.03483 ( 287) hydrogen bonds : angle 3.58686 ( 822) *********************** 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 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.208 Fit side-chains REVERT: A 426 TYR cc_start: 0.7863 (m-10) cc_final: 0.7465 (m-80) REVERT: B 18 LEU cc_start: 0.8017 (mp) cc_final: 0.7718 (tt) REVERT: B 30 LYS cc_start: 0.8343 (pttm) cc_final: 0.7939 (ptmt) REVERT: B 55 GLU cc_start: 0.9050 (mp0) cc_final: 0.8625 (mp0) REVERT: B 59 TYR cc_start: 0.8959 (m-80) cc_final: 0.8452 (m-80) REVERT: C 3 GLN cc_start: 0.8487 (mp-120) cc_final: 0.8088 (mm-40) outliers start: 18 outliers final: 13 residues processed: 107 average time/residue: 0.0682 time to fit residues: 9.7203 Evaluate side-chains 106 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 494 ILE Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 HIS 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 70 SER 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 43 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 = 0.3492 r_free = 0.3492 target = 0.110962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093272 restraints weight = 10213.548| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.66 r_work: 0.3104 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6106 Z= 0.163 Angle : 0.533 7.591 8278 Z= 0.288 Chirality : 0.042 0.193 898 Planarity : 0.003 0.040 1020 Dihedral : 5.895 38.970 939 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.72 % Allowed : 17.15 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.31), residues: 723 helix: 2.31 (0.29), residues: 312 sheet: 0.65 (0.42), residues: 141 loop : -1.38 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 27 TYR 0.012 0.002 TYR A 414 PHE 0.011 0.002 PHE A 385 TRP 0.010 0.001 TRP A 472 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 6104) covalent geometry : angle 0.53326 ( 8274) SS BOND : bond 0.00461 ( 2) SS BOND : angle 0.56932 ( 4) hydrogen bonds : bond 0.04091 ( 287) hydrogen bonds : angle 3.75608 ( 822) *********************** 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 113 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.160 Fit side-chains REVERT: A 426 TYR cc_start: 0.8117 (m-10) cc_final: 0.7759 (m-80) REVERT: B 30 LYS cc_start: 0.8606 (pttm) cc_final: 0.8197 (ptmt) REVERT: B 55 GLU cc_start: 0.9034 (mp0) cc_final: 0.8692 (mp0) REVERT: C 3 GLN cc_start: 0.8395 (mp-120) cc_final: 0.7920 (mm-40) REVERT: C 71 ARG cc_start: 0.7806 (mtm110) cc_final: 0.7499 (mtm110) outliers start: 17 outliers final: 13 residues processed: 109 average time/residue: 0.0800 time to fit residues: 11.3894 Evaluate side-chains 104 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 433 VAL 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 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 58 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.113020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.095293 restraints weight = 10158.995| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.66 r_work: 0.3131 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6106 Z= 0.117 Angle : 0.515 8.041 8278 Z= 0.273 Chirality : 0.041 0.228 898 Planarity : 0.003 0.048 1020 Dihedral : 5.727 37.775 939 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.21 % Allowed : 18.11 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.31), residues: 723 helix: 2.37 (0.29), residues: 312 sheet: 0.60 (0.42), residues: 141 loop : -1.33 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 27 TYR 0.020 0.001 TYR C 105 PHE 0.016 0.001 PHE B 67 TRP 0.008 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6104) covalent geometry : angle 0.51456 ( 8274) SS BOND : bond 0.00391 ( 2) SS BOND : angle 0.60663 ( 4) hydrogen bonds : bond 0.03614 ( 287) hydrogen bonds : angle 3.66465 ( 822) *********************** 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 114 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.152 Fit side-chains REVERT: A 311 MET cc_start: 0.6437 (mtt) cc_final: 0.6096 (mtt) REVERT: A 426 TYR cc_start: 0.8094 (m-10) cc_final: 0.7742 (m-80) REVERT: B 30 LYS cc_start: 0.8538 (pttm) cc_final: 0.8121 (ptmt) REVERT: B 55 GLU cc_start: 0.9032 (mp0) cc_final: 0.8593 (mp0) REVERT: B 75 LYS cc_start: 0.8910 (mtmt) cc_final: 0.8651 (pttm) REVERT: C 3 GLN cc_start: 0.8450 (mp-120) cc_final: 0.7911 (mm-40) outliers start: 20 outliers final: 14 residues processed: 109 average time/residue: 0.0825 time to fit residues: 11.7824 Evaluate side-chains 108 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.227 ------------------------------------------------------------------------------- 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 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 A residue 552 HIS 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 33 THR Chi-restraints excluded: chain C residue 70 SER 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 13 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.109801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092089 restraints weight = 10177.260| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.65 r_work: 0.3079 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6106 Z= 0.165 Angle : 0.554 8.642 8278 Z= 0.296 Chirality : 0.042 0.206 898 Planarity : 0.003 0.031 1020 Dihedral : 5.999 43.815 939 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.53 % Allowed : 17.15 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.31), residues: 723 helix: 2.30 (0.29), residues: 312 sheet: 0.51 (0.42), residues: 141 loop : -1.48 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 27 TYR 0.012 0.001 TYR A 414 PHE 0.023 0.001 PHE B 67 TRP 0.009 0.001 TRP A 246 HIS 0.001 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 6104) covalent geometry : angle 0.55425 ( 8274) SS BOND : bond 0.00476 ( 2) SS BOND : angle 0.60431 ( 4) hydrogen bonds : bond 0.04090 ( 287) hydrogen bonds : angle 3.76311 ( 822) *********************** 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 : 0.244 Fit side-chains REVERT: A 311 MET cc_start: 0.6442 (mtt) cc_final: 0.6114 (mtt) REVERT: A 426 TYR cc_start: 0.8220 (m-10) cc_final: 0.7971 (m-80) REVERT: B 30 LYS cc_start: 0.8766 (pttm) cc_final: 0.8402 (ptmt) REVERT: B 55 GLU cc_start: 0.9027 (mp0) cc_final: 0.8593 (mp0) REVERT: B 75 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8592 (pttm) REVERT: C 3 GLN cc_start: 0.8410 (mp-120) cc_final: 0.7827 (mm110) outliers start: 22 outliers final: 21 residues processed: 107 average time/residue: 0.0725 time to fit residues: 10.3732 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 : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 130 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 433 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 523 ILE Chi-restraints excluded: chain A residue 526 VAL Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 552 HIS 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 85 LEU 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 28 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 38 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094056 restraints weight = 10161.262| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.65 r_work: 0.3118 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6106 Z= 0.117 Angle : 0.537 8.769 8278 Z= 0.284 Chirality : 0.041 0.209 898 Planarity : 0.003 0.031 1020 Dihedral : 5.907 46.377 939 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.72 % Allowed : 18.11 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.30), residues: 723 helix: 2.32 (0.29), residues: 313 sheet: 0.42 (0.42), residues: 140 loop : -1.50 (0.33), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 27 TYR 0.019 0.001 TYR C 105 PHE 0.015 0.001 PHE B 67 TRP 0.009 0.001 TRP A 246 HIS 0.002 0.001 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6104) covalent geometry : angle 0.53736 ( 8274) SS BOND : bond 0.00384 ( 2) SS BOND : angle 0.66536 ( 4) hydrogen bonds : bond 0.03657 ( 287) hydrogen bonds : angle 3.68449 ( 822) *********************** 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 117 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.201 Fit side-chains REVERT: A 311 MET cc_start: 0.6226 (mtt) cc_final: 0.5993 (mtt) REVERT: A 426 TYR cc_start: 0.8177 (m-10) cc_final: 0.7906 (m-80) REVERT: B 30 LYS cc_start: 0.8744 (pttm) cc_final: 0.8348 (ptmt) REVERT: B 55 GLU cc_start: 0.9000 (mp0) cc_final: 0.8554 (mp0) REVERT: B 75 LYS cc_start: 0.8847 (mtmt) cc_final: 0.8620 (pttm) REVERT: C 3 GLN cc_start: 0.8431 (mp-120) cc_final: 0.7843 (mm110) outliers start: 17 outliers final: 14 residues processed: 112 average time/residue: 0.0751 time to fit residues: 11.2122 Evaluate side-chains 107 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.110607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093026 restraints weight = 10224.525| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.64 r_work: 0.3101 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6106 Z= 0.136 Angle : 0.544 9.099 8278 Z= 0.289 Chirality : 0.041 0.210 898 Planarity : 0.003 0.031 1020 Dihedral : 5.961 50.376 939 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.04 % Allowed : 18.75 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.31), residues: 723 helix: 2.32 (0.29), residues: 312 sheet: 0.37 (0.42), residues: 140 loop : -1.50 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 27 TYR 0.012 0.001 TYR A 414 PHE 0.018 0.001 PHE B 67 TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 6104) covalent geometry : angle 0.54410 ( 8274) SS BOND : bond 0.00400 ( 2) SS BOND : angle 0.66806 ( 4) hydrogen bonds : bond 0.03764 ( 287) hydrogen bonds : angle 3.70056 ( 822) ********************** 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 118 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.215 Fit side-chains REVERT: A 311 MET cc_start: 0.6298 (mtt) cc_final: 0.6066 (mtt) REVERT: A 426 TYR cc_start: 0.8185 (m-10) cc_final: 0.7975 (m-80) REVERT: A 481 MET cc_start: 0.8404 (mtp) cc_final: 0.8099 (mtp) REVERT: B 5 VAL cc_start: 0.8862 (t) cc_final: 0.8581 (m) REVERT: B 30 LYS cc_start: 0.8805 (pttm) cc_final: 0.8436 (ptmt) REVERT: B 55 GLU cc_start: 0.9022 (mp0) cc_final: 0.8585 (mp0) REVERT: B 75 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8561 (pttm) REVERT: C 3 GLN cc_start: 0.8415 (mp-120) cc_final: 0.7817 (mm110) outliers start: 19 outliers final: 18 residues processed: 112 average time/residue: 0.0731 time to fit residues: 10.9941 Evaluate side-chains 116 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 0.255 ------------------------------------------------------------------------------- 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 285 ASP 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 433 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 4 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 31 optimal weight: 0.4980 chunk 66 optimal weight: 0.3980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.112363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.094862 restraints weight = 10090.646| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.62 r_work: 0.3129 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6106 Z= 0.112 Angle : 0.534 8.963 8278 Z= 0.282 Chirality : 0.041 0.211 898 Planarity : 0.003 0.032 1020 Dihedral : 5.921 51.556 939 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.56 % Allowed : 19.23 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.30), residues: 723 helix: 2.33 (0.28), residues: 313 sheet: 0.38 (0.40), residues: 149 loop : -1.57 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 27 TYR 0.018 0.001 TYR C 105 PHE 0.014 0.001 PHE B 67 TRP 0.009 0.001 TRP A 246 HIS 0.001 0.000 HIS A 174 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 6104) covalent geometry : angle 0.53416 ( 8274) SS BOND : bond 0.00368 ( 2) SS BOND : angle 0.67695 ( 4) hydrogen bonds : bond 0.03570 ( 287) hydrogen bonds : angle 3.64798 ( 822) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.00 seconds wall clock time: 24 minutes 23.63 seconds (1463.63 seconds total)