Starting phenix.real_space_refine on Thu Jul 2 03:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n0c_24103/07_2026/7n0c_24103.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0c_24103/07_2026/7n0c_24103.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7n0c_24103/07_2026/7n0c_24103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0c_24103/07_2026/7n0c_24103.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n0c_24103/07_2026/7n0c_24103.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n0c_24103/07_2026/7n0c_24103.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7n0c_24103/07_2026/7n0c_24103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0c_24103/07_2026/7n0c_24103.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 49 5.49 5 Mg 2 5.21 5 S 52 5.16 5 C 3685 2.51 5 N 1033 2.21 5 O 1262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6088 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 955 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 7, 'TRANS': 123} Chain: "B" Number of atoms: 4090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4090 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 26, 'TRANS': 486} Chain breaks: 1 Chain: "T" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 529 Classifications: {'RNA': 25} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna2p': 1, 'rna3p': 23} Chain: "D" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 506 Classifications: {'RNA': 24} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 12} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 2, ' ZN': 3} Classifications: {'undetermined': 5, 'water': 1} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 520 SG CYS A 74 40.023 24.791 92.919 1.00 51.61 S ATOM 546 SG CYS A 77 36.858 25.756 93.856 1.00 51.71 S ATOM 651 SG CYS A 90 37.756 22.498 94.187 1.00 57.18 S ATOM 854 SG CYS A 117 52.155 10.429 99.974 1.00112.87 S ATOM 874 SG CYS A 120 52.595 10.897 103.370 1.00118.76 S ATOM 935 SG CYS A 128 55.207 11.780 101.062 1.00109.13 S ATOM 947 SG CYS A 130 55.533 8.590 102.165 1.00128.22 S ATOM 2582 SG CYS B 207 44.467 25.564 61.321 1.00 62.28 S ATOM 2602 SG CYS B 210 45.850 26.017 57.879 1.00 73.07 S ATOM 2723 SG CYS B 226 43.066 27.801 59.072 1.00 56.89 S ATOM 3023 SG CYS B 261 24.861 55.828 57.812 1.00 65.13 S ATOM 3153 SG CYS B 279 27.911 54.398 59.550 1.00 44.17 S ATOM 4543 SG CYS B 452 49.557 45.528 11.477 1.00134.04 S ATOM 4657 SG CYS B 477 45.734 45.992 12.975 1.00138.24 S ATOM 4699 SG CYS B 484 48.139 43.581 13.594 1.00139.40 S Time building chain proxies: 1.01, per 1000 atoms: 0.17 Number of scatterers: 6088 At special positions: 0 Unit cell: (70.488, 89.712, 144.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 52 16.00 P 49 15.00 Mg 2 11.99 O 1262 8.00 N 1033 7.00 C 3685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 213.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 201 " pdb="ZN ZN A 201 " - pdb=" NE2 HIS A 83 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 77 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 90 " pdb="ZN ZN A 201 " - pdb=" SG CYS A 74 " pdb=" ZN A 202 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 128 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 130 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 120 " pdb="ZN ZN A 202 " - pdb=" SG CYS A 117 " pdb=" ZN B 603 " pdb="ZN ZN B 603 " - pdb=" ND1 HIS B 229 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 226 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 210 " pdb="ZN ZN B 603 " - pdb=" SG CYS B 207 " pdb=" ZN B 604 " pdb="ZN ZN B 604 " - pdb=" ND1 HIS B 264 " pdb="ZN ZN B 604 " - pdb=" NE2 HIS B 257 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 279 " pdb="ZN ZN B 604 " - pdb=" SG CYS B 261 " pdb=" ZN B 605 " pdb="ZN ZN B 605 " - pdb=" ND1 HIS B 487 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 484 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 477 " pdb="ZN ZN B 605 " - pdb=" SG CYS B 452 " Number of angles added : 17 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1204 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 8 sheets defined 26.6% alpha, 12.1% beta 23 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 22 through 33 Processing helix chain 'A' and resid 74 through 80 Processing helix chain 'A' and resid 85 through 89 removed outlier: 4.249A pdb=" N PHE A 89 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 109 through 114 removed outlier: 4.067A pdb=" N LYS A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.595A pdb=" N VAL B 29 " --> pdb=" O HIS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 169 through 174 Processing helix chain 'B' and resid 187 through 194 removed outlier: 3.844A pdb=" N ALA B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 248 removed outlier: 3.850A pdb=" N GLY B 248 " --> pdb=" O GLN B 245 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 245 through 248' Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.654A pdb=" N ASP B 258 " --> pdb=" O GLN B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 274 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.841A pdb=" N CYS B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 325 removed outlier: 3.584A pdb=" N ASN B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 318 " --> pdb=" O HIS B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'B' and resid 414 through 416 No H-bonds generated for 'chain 'B' and resid 414 through 416' Processing helix chain 'B' and resid 432 through 437 removed outlier: 3.931A pdb=" N VAL B 437 " --> pdb=" O SER B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 480 removed outlier: 3.589A pdb=" N GLY B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 505 removed outlier: 4.313A pdb=" N ASN B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.754A pdb=" N ASN B 521 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 removed outlier: 4.365A pdb=" N TYR B 124 " --> pdb=" O ILE B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118 removed outlier: 5.519A pdb=" N CYS B 94 " --> pdb=" O PRO B 106 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 223 through 225 removed outlier: 3.726A pdb=" N THR B 223 " --> pdb=" O SER B 218 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 364 through 365 removed outlier: 7.020A pdb=" N LEU B 329 " --> pdb=" O LYS B 349 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N TYR B 351 " --> pdb=" O LEU B 329 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP B 331 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 381 " --> pdb=" O VAL B 328 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 397 through 401 Processing sheet with id=AA7, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA8, first strand: chain 'B' and resid 446 through 447 removed outlier: 5.938A pdb=" N TYR B 446 " --> pdb=" O ILE B 474 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 125 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 53 hydrogen bonds 106 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 0.65 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 860 1.29 - 1.42: 2016 1.42 - 1.56: 3298 1.56 - 1.69: 97 1.69 - 1.83: 68 Bond restraints: 6339 Sorted by residual: bond pdb=" C PRO B 106 " pdb=" O PRO B 106 " ideal model delta sigma weight residual 1.233 1.151 0.082 1.06e-02 8.90e+03 6.06e+01 bond pdb=" CA PRO B 106 " pdb=" CB PRO B 106 " ideal model delta sigma weight residual 1.533 1.485 0.048 1.26e-02 6.30e+03 1.44e+01 bond pdb=" N LEU B 105 " pdb=" CA LEU B 105 " ideal model delta sigma weight residual 1.452 1.499 -0.047 1.41e-02 5.03e+03 1.12e+01 bond pdb=" C ASN B 104 " pdb=" O ASN B 104 " ideal model delta sigma weight residual 1.234 1.195 0.039 1.19e-02 7.06e+03 1.06e+01 bond pdb=" C LEU B 105 " pdb=" N PRO B 106 " ideal model delta sigma weight residual 1.334 1.368 -0.034 1.11e-02 8.12e+03 9.49e+00 ... (remaining 6334 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 8233 1.82 - 3.63: 502 3.63 - 5.45: 81 5.45 - 7.27: 19 7.27 - 9.09: 6 Bond angle restraints: 8841 Sorted by residual: angle pdb=" CA PRO B 106 " pdb=" C PRO B 106 " pdb=" O PRO B 106 " ideal model delta sigma weight residual 120.97 111.88 9.09 1.17e+00 7.31e-01 6.03e+01 angle pdb=" C PRO B 106 " pdb=" CA PRO B 106 " pdb=" CB PRO B 106 " ideal model delta sigma weight residual 111.11 103.39 7.72 1.17e+00 7.31e-01 4.35e+01 angle pdb=" CA PRO B 106 " pdb=" C PRO B 106 " pdb=" N LEU B 107 " ideal model delta sigma weight residual 115.93 123.67 -7.74 1.26e+00 6.30e-01 3.78e+01 angle pdb=" CA LEU B 105 " pdb=" C LEU B 105 " pdb=" N PRO B 106 " ideal model delta sigma weight residual 117.67 123.60 -5.93 1.01e+00 9.80e-01 3.45e+01 angle pdb=" N VAL B 167 " pdb=" CA VAL B 167 " pdb=" C VAL B 167 " ideal model delta sigma weight residual 112.90 107.43 5.47 9.60e-01 1.09e+00 3.24e+01 ... (remaining 8836 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 3557 34.34 - 68.68: 62 68.68 - 103.02: 4 103.02 - 137.36: 0 137.36 - 171.70: 1 Dihedral angle restraints: 3624 sinusoidal: 1749 harmonic: 1875 Sorted by residual: dihedral pdb=" O4' U T 6 " pdb=" C1' U T 6 " pdb=" N1 U T 6 " pdb=" C2 U T 6 " ideal model delta sinusoidal sigma weight residual 232.00 60.30 171.70 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" CA HIS B 268 " pdb=" C HIS B 268 " pdb=" N VAL B 269 " pdb=" CA VAL B 269 " ideal model delta harmonic sigma weight residual 180.00 156.65 23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA TYR B 237 " pdb=" C TYR B 237 " pdb=" N ASN B 238 " pdb=" CA ASN B 238 " ideal model delta harmonic sigma weight residual -180.00 -159.88 -20.12 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 3621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 671 0.041 - 0.083: 237 0.083 - 0.124: 74 0.124 - 0.166: 21 0.166 - 0.207: 12 Chirality restraints: 1015 Sorted by residual: chirality pdb=" CA ASN B 478 " pdb=" N ASN B 478 " pdb=" C ASN B 478 " pdb=" CB ASN B 478 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA CYS B 210 " pdb=" N CYS B 210 " pdb=" C CYS B 210 " pdb=" CB CYS B 210 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ASP B 415 " pdb=" N ASP B 415 " pdb=" C ASP B 415 " pdb=" CB ASP B 415 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 1012 not shown) Planarity restraints: 953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS B 487 " -0.060 2.00e-02 2.50e+03 4.49e-02 3.02e+01 pdb=" CG HIS B 487 " 0.061 2.00e-02 2.50e+03 pdb=" ND1 HIS B 487 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 HIS B 487 " 0.032 2.00e-02 2.50e+03 pdb=" CE1 HIS B 487 " -0.039 2.00e-02 2.50e+03 pdb=" NE2 HIS B 487 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 229 " -0.053 2.00e-02 2.50e+03 4.01e-02 2.41e+01 pdb=" CG HIS B 229 " 0.054 2.00e-02 2.50e+03 pdb=" ND1 HIS B 229 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 HIS B 229 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS B 229 " -0.037 2.00e-02 2.50e+03 pdb=" NE2 HIS B 229 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 83 " 0.044 2.00e-02 2.50e+03 3.24e-02 1.58e+01 pdb=" CG HIS A 83 " -0.047 2.00e-02 2.50e+03 pdb=" ND1 HIS A 83 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 HIS A 83 " -0.019 2.00e-02 2.50e+03 pdb=" CE1 HIS A 83 " 0.028 2.00e-02 2.50e+03 pdb=" NE2 HIS A 83 " 0.019 2.00e-02 2.50e+03 ... (remaining 950 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 510 2.72 - 3.27: 5827 3.27 - 3.81: 10466 3.81 - 4.36: 12799 4.36 - 4.90: 20376 Nonbonded interactions: 49978 Sorted by model distance: nonbonded pdb=" OD1 ASP B 90 " pdb="MG MG B 602 " model vdw 2.180 2.170 nonbonded pdb=" OD2 ASP B 90 " pdb="MG MG B 601 " model vdw 2.216 2.170 nonbonded pdb=" O ILE B 80 " pdb=" OH TYR B 296 " model vdw 2.221 3.040 nonbonded pdb=" OG SER B 171 " pdb=" O TRP B 227 " model vdw 2.226 3.040 nonbonded pdb=" OE1 GLU B 302 " pdb=" ND2 ASN B 422 " model vdw 2.257 3.120 ... (remaining 49973 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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 : 0.014 0.334 6359 Z= 0.557 Angle : 1.156 25.154 8858 Z= 0.624 Chirality : 0.052 0.207 1015 Planarity : 0.007 0.059 953 Dihedral : 13.783 171.703 2420 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.80 (0.27), residues: 638 helix: -3.43 (0.29), residues: 142 sheet: -2.66 (0.62), residues: 49 loop : -2.34 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 163 TYR 0.022 0.002 TYR A 76 PHE 0.040 0.003 PHE A 19 TRP 0.010 0.002 TRP B 385 HIS 0.011 0.003 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00862 / 0.43 ( 6339) covalent geometry : angle 0.99601 / 0.61 ( 8841) hydrogen bonds : bond 0.18771 / 12.69 ( 178) hydrogen bonds : angle 7.65072 / 5.27 ( 430) metal coordination : bond 0.20625 / 12.88 ( 20) metal coordination : angle 13.43401 / 10.28 ( 17) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7959 (mmtp) REVERT: A 98 GLN cc_start: 0.8060 (mp-120) cc_final: 0.7753 (mm110) REVERT: A 114 ASN cc_start: 0.8736 (m-40) cc_final: 0.8524 (m110) REVERT: B 58 MET cc_start: 0.8765 (mtp) cc_final: 0.8334 (mtp) REVERT: B 169 MET cc_start: 0.8659 (ttp) cc_final: 0.7963 (tmm) REVERT: B 330 HIS cc_start: 0.7916 (m-70) cc_final: 0.6908 (m-70) REVERT: B 499 ASN cc_start: 0.7842 (m-40) cc_final: 0.7559 (m-40) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.0614 time to fit residues: 8.4264 Evaluate side-chains 88 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 HIS B 499 ASN B 521 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.176785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120633 restraints weight = 7428.173| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.07 r_work: 0.3037 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6359 Z= 0.170 Angle : 0.598 9.681 8858 Z= 0.299 Chirality : 0.040 0.148 1015 Planarity : 0.005 0.055 953 Dihedral : 10.436 172.518 1275 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.17 % Allowed : 10.31 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.98 (0.29), residues: 638 helix: -2.02 (0.39), residues: 139 sheet: -3.11 (0.49), residues: 68 loop : -1.84 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 78 TYR 0.023 0.001 TYR B 370 PHE 0.016 0.002 PHE A 19 TRP 0.008 0.001 TRP B 385 HIS 0.006 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 6339) covalent geometry : angle 0.56227 / 0.30 ( 8841) hydrogen bonds : bond 0.04080 / 2.64 ( 178) hydrogen bonds : angle 5.08461 / 3.55 ( 430) metal coordination : bond 0.01784 / 0.93 ( 20) metal coordination : angle 4.69720 / 3.71 ( 17) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8379 (t) cc_final: 0.8177 (t) REVERT: A 95 LYS cc_start: 0.7739 (mmtt) cc_final: 0.7521 (mmtp) REVERT: A 98 GLN cc_start: 0.8304 (mp-120) cc_final: 0.7857 (mm-40) REVERT: A 114 ASN cc_start: 0.8818 (m-40) cc_final: 0.8452 (m110) REVERT: B 58 MET cc_start: 0.9053 (mtp) cc_final: 0.8654 (mtp) REVERT: B 61 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8781 (mtpp) REVERT: B 169 MET cc_start: 0.8857 (ttp) cc_final: 0.8517 (tmm) REVERT: B 185 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8638 (mt) REVERT: B 330 HIS cc_start: 0.7541 (m-70) cc_final: 0.6415 (m170) REVERT: B 384 PHE cc_start: 0.9055 (m-80) cc_final: 0.8817 (m-80) REVERT: B 391 ARG cc_start: 0.8293 (ttm170) cc_final: 0.7774 (mtp180) REVERT: B 395 ASN cc_start: 0.8471 (p0) cc_final: 0.8142 (p0) REVERT: B 499 ASN cc_start: 0.7790 (m110) cc_final: 0.7499 (m-40) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.0608 time to fit residues: 8.7483 Evaluate side-chains 97 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 15 optimal weight: 0.0980 chunk 54 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.0020 chunk 32 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 5 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS B 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.180951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.124233 restraints weight = 7390.897| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.57 r_work: 0.3158 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6359 Z= 0.092 Angle : 0.514 6.056 8858 Z= 0.255 Chirality : 0.038 0.144 1015 Planarity : 0.004 0.031 953 Dihedral : 10.178 173.178 1275 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.07 % Allowed : 11.75 % Favored : 85.17 % 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: -2.10 (0.32), residues: 638 helix: -1.01 (0.44), residues: 139 sheet: -2.36 (0.57), residues: 67 loop : -1.40 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 404 TYR 0.012 0.001 TYR B 370 PHE 0.010 0.001 PHE B 133 TRP 0.007 0.001 TRP B 520 HIS 0.003 0.000 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.09 ( 6339) covalent geometry : angle 0.50089 / 0.25 ( 8841) hydrogen bonds : bond 0.03187 / 2.04 ( 178) hydrogen bonds : angle 4.57675 / 3.15 ( 430) metal coordination : bond 0.00524 / 0.31 ( 20) metal coordination : angle 2.64115 / 2.07 ( 17) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8172 (t) cc_final: 0.7911 (t) REVERT: A 95 LYS cc_start: 0.7619 (mmtt) cc_final: 0.7171 (mttm) REVERT: A 98 GLN cc_start: 0.8348 (mp-120) cc_final: 0.8068 (mm-40) REVERT: A 114 ASN cc_start: 0.8744 (m-40) cc_final: 0.8508 (m110) REVERT: A 126 TYR cc_start: 0.6697 (m-80) cc_final: 0.6436 (m-80) REVERT: B 58 MET cc_start: 0.9111 (mtp) cc_final: 0.8735 (mtp) REVERT: B 61 LYS cc_start: 0.9076 (mtpt) cc_final: 0.8710 (mtpp) REVERT: B 169 MET cc_start: 0.8902 (ttp) cc_final: 0.8598 (ptm) REVERT: B 330 HIS cc_start: 0.7633 (m-70) cc_final: 0.6902 (m170) REVERT: B 384 PHE cc_start: 0.8993 (m-80) cc_final: 0.8761 (m-80) REVERT: B 389 VAL cc_start: 0.8435 (p) cc_final: 0.8115 (p) REVERT: B 391 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7756 (mtp180) REVERT: B 395 ASN cc_start: 0.8502 (p0) cc_final: 0.8071 (p0) REVERT: B 499 ASN cc_start: 0.7783 (m110) cc_final: 0.7550 (m110) REVERT: B 512 LYS cc_start: 0.8665 (mmtm) cc_final: 0.8446 (mmtm) outliers start: 17 outliers final: 10 residues processed: 108 average time/residue: 0.0560 time to fit residues: 8.2701 Evaluate side-chains 106 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 382 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 59 optimal weight: 9.9990 chunk 3 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 67 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 = 0.4111 r_free = 0.4111 target = 0.178487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.121208 restraints weight = 7377.082| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.55 r_work: 0.3118 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6359 Z= 0.134 Angle : 0.512 5.952 8858 Z= 0.258 Chirality : 0.039 0.139 1015 Planarity : 0.004 0.032 953 Dihedral : 10.065 173.286 1275 Min Nonbonded Distance : 1.499 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.07 % Allowed : 11.93 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.32), residues: 638 helix: -0.98 (0.44), residues: 143 sheet: -2.24 (0.60), residues: 62 loop : -1.37 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 404 TYR 0.007 0.001 TYR B 370 PHE 0.016 0.001 PHE B 350 TRP 0.006 0.001 TRP B 520 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 ( 6339) covalent geometry : angle 0.50165 / 0.26 ( 8841) hydrogen bonds : bond 0.03197 / 1.99 ( 178) hydrogen bonds : angle 4.38092 / 3.02 ( 430) metal coordination : bond 0.00965 / 0.59 ( 20) metal coordination : angle 2.39886 / 1.86 ( 17) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8108 (t) cc_final: 0.7815 (t) REVERT: A 95 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7283 (mttm) REVERT: A 98 GLN cc_start: 0.8504 (mp-120) cc_final: 0.8144 (mm-40) REVERT: A 114 ASN cc_start: 0.8759 (m-40) cc_final: 0.8515 (m110) REVERT: A 126 TYR cc_start: 0.6739 (m-80) cc_final: 0.6405 (m-80) REVERT: B 58 MET cc_start: 0.9161 (mtp) cc_final: 0.8790 (mtp) REVERT: B 61 LYS cc_start: 0.9073 (mtpt) cc_final: 0.8625 (mtpp) REVERT: B 169 MET cc_start: 0.8924 (ttp) cc_final: 0.8618 (ptm) REVERT: B 185 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8611 (mt) REVERT: B 330 HIS cc_start: 0.7782 (m-70) cc_final: 0.6867 (m170) REVERT: B 334 ASN cc_start: 0.8410 (t0) cc_final: 0.8060 (p0) REVERT: B 373 HIS cc_start: 0.8428 (m90) cc_final: 0.8046 (m90) REVERT: B 391 ARG cc_start: 0.8277 (ttm170) cc_final: 0.7870 (mtp180) REVERT: B 395 ASN cc_start: 0.8536 (p0) cc_final: 0.8103 (p0) REVERT: B 398 VAL cc_start: 0.9103 (t) cc_final: 0.8734 (p) REVERT: B 445 PHE cc_start: 0.8887 (p90) cc_final: 0.8635 (p90) REVERT: B 499 ASN cc_start: 0.7735 (m110) cc_final: 0.7463 (m-40) outliers start: 17 outliers final: 14 residues processed: 106 average time/residue: 0.0505 time to fit residues: 7.3813 Evaluate side-chains 109 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 67 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 = 0.4073 r_free = 0.4073 target = 0.176588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118194 restraints weight = 7429.576| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.67 r_work: 0.3050 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6359 Z= 0.157 Angle : 0.520 5.258 8858 Z= 0.265 Chirality : 0.039 0.144 1015 Planarity : 0.004 0.026 953 Dihedral : 10.049 173.181 1275 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.98 % Allowed : 12.30 % Favored : 83.73 % 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: -1.92 (0.32), residues: 638 helix: -0.89 (0.45), residues: 143 sheet: -2.15 (0.62), residues: 60 loop : -1.32 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 404 TYR 0.007 0.001 TYR B 51 PHE 0.022 0.002 PHE B 444 TRP 0.006 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 ( 6339) covalent geometry : angle 0.51033 / 0.26 ( 8841) hydrogen bonds : bond 0.03221 / 1.97 ( 178) hydrogen bonds : angle 4.35387 / 3.02 ( 430) metal coordination : bond 0.01173 / 0.73 ( 20) metal coordination : angle 2.31737 / 1.78 ( 17) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8014 (t) cc_final: 0.7742 (t) REVERT: A 114 ASN cc_start: 0.8711 (m-40) cc_final: 0.8324 (m110) REVERT: B 58 MET cc_start: 0.9016 (mtp) cc_final: 0.8622 (mtp) REVERT: B 61 LYS cc_start: 0.9047 (mtpt) cc_final: 0.8588 (mtpp) REVERT: B 169 MET cc_start: 0.8829 (ttp) cc_final: 0.8507 (ptm) REVERT: B 185 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8458 (mt) REVERT: B 315 MET cc_start: 0.8109 (tpp) cc_final: 0.7880 (tpp) REVERT: B 330 HIS cc_start: 0.7561 (m-70) cc_final: 0.6539 (m-70) REVERT: B 373 HIS cc_start: 0.8408 (m90) cc_final: 0.8026 (m90) REVERT: B 391 ARG cc_start: 0.8198 (ttm170) cc_final: 0.7701 (mtp180) REVERT: B 395 ASN cc_start: 0.8519 (p0) cc_final: 0.8065 (p0) REVERT: B 398 VAL cc_start: 0.9030 (t) cc_final: 0.8728 (p) outliers start: 22 outliers final: 19 residues processed: 105 average time/residue: 0.0560 time to fit residues: 8.2050 Evaluate side-chains 111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 42 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 10 optimal weight: 0.0370 chunk 16 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 ASN B 499 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.179473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120636 restraints weight = 7324.395| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.66 r_work: 0.3088 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6359 Z= 0.101 Angle : 0.480 6.487 8858 Z= 0.245 Chirality : 0.038 0.139 1015 Planarity : 0.003 0.025 953 Dihedral : 9.960 173.443 1275 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.44 % Allowed : 13.38 % Favored : 83.18 % 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: -1.60 (0.33), residues: 638 helix: -0.45 (0.47), residues: 138 sheet: -2.12 (0.57), residues: 69 loop : -1.10 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.007 0.001 TYR B 420 PHE 0.016 0.001 PHE B 350 TRP 0.008 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 6339) covalent geometry : angle 0.47443 / 0.24 ( 8841) hydrogen bonds : bond 0.03038 / 1.86 ( 178) hydrogen bonds : angle 4.21147 / 2.89 ( 430) metal coordination : bond 0.00560 / 0.33 ( 20) metal coordination : angle 1.75954 / 1.34 ( 17) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.7933 (t) cc_final: 0.7645 (t) REVERT: A 114 ASN cc_start: 0.8741 (m-40) cc_final: 0.8376 (m110) REVERT: B 58 MET cc_start: 0.8979 (mtp) cc_final: 0.8481 (mtp) REVERT: B 61 LYS cc_start: 0.8935 (mtpt) cc_final: 0.8456 (mtpp) REVERT: B 169 MET cc_start: 0.8793 (ttp) cc_final: 0.8474 (ptm) REVERT: B 185 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8461 (mt) REVERT: B 315 MET cc_start: 0.7967 (tpp) cc_final: 0.7742 (tpp) REVERT: B 330 HIS cc_start: 0.7458 (m-70) cc_final: 0.6492 (m-70) REVERT: B 334 ASN cc_start: 0.8303 (t0) cc_final: 0.7938 (p0) REVERT: B 373 HIS cc_start: 0.8362 (m90) cc_final: 0.7976 (m90) REVERT: B 391 ARG cc_start: 0.8146 (ttm170) cc_final: 0.7672 (mtp180) REVERT: B 395 ASN cc_start: 0.8574 (p0) cc_final: 0.8121 (p0) REVERT: B 398 VAL cc_start: 0.8962 (t) cc_final: 0.8701 (p) REVERT: B 445 PHE cc_start: 0.8799 (p90) cc_final: 0.8390 (p90) outliers start: 19 outliers final: 13 residues processed: 111 average time/residue: 0.0482 time to fit residues: 7.5665 Evaluate side-chains 111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 0.9980 chunk 41 optimal weight: 0.0010 chunk 33 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.0020 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.190128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.135345 restraints weight = 7508.139| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 2.69 r_work: 0.3267 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6359 Z= 0.114 Angle : 0.488 6.891 8858 Z= 0.248 Chirality : 0.038 0.140 1015 Planarity : 0.003 0.026 953 Dihedral : 9.885 173.589 1275 Min Nonbonded Distance : 1.125 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.62 % Allowed : 14.65 % Favored : 81.74 % 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: -1.57 (0.32), residues: 638 helix: -0.47 (0.45), residues: 143 sheet: -1.98 (0.60), residues: 62 loop : -1.12 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.009 0.001 TYR B 260 PHE 0.012 0.001 PHE B 384 TRP 0.010 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 6339) covalent geometry : angle 0.48266 / 0.25 ( 8841) hydrogen bonds : bond 0.03054 / 1.83 ( 178) hydrogen bonds : angle 4.14646 / 2.84 ( 430) metal coordination : bond 0.00705 / 0.42 ( 20) metal coordination : angle 1.75895 / 1.34 ( 17) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8130 (t) cc_final: 0.7847 (t) REVERT: B 58 MET cc_start: 0.9010 (mtp) cc_final: 0.8459 (mtp) REVERT: B 61 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8635 (mtpp) REVERT: B 169 MET cc_start: 0.8723 (ttp) cc_final: 0.8434 (ptm) REVERT: B 185 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8644 (mt) REVERT: B 330 HIS cc_start: 0.7623 (m-70) cc_final: 0.6876 (m-70) REVERT: B 352 ASP cc_start: 0.7031 (t0) cc_final: 0.6759 (t70) REVERT: B 373 HIS cc_start: 0.8402 (m90) cc_final: 0.8038 (m90) REVERT: B 391 ARG cc_start: 0.8339 (ttm170) cc_final: 0.7992 (mtp180) REVERT: B 395 ASN cc_start: 0.8595 (p0) cc_final: 0.8301 (p0) REVERT: B 445 PHE cc_start: 0.8813 (p90) cc_final: 0.8506 (p90) outliers start: 20 outliers final: 16 residues processed: 110 average time/residue: 0.0523 time to fit residues: 7.9382 Evaluate side-chains 113 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.189210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134408 restraints weight = 7469.487| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.61 r_work: 0.3264 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6359 Z= 0.138 Angle : 0.511 6.212 8858 Z= 0.260 Chirality : 0.039 0.143 1015 Planarity : 0.003 0.026 953 Dihedral : 9.890 173.474 1275 Min Nonbonded Distance : 1.113 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.62 % Allowed : 15.73 % Favored : 80.65 % 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: -1.48 (0.32), residues: 638 helix: -0.40 (0.45), residues: 143 sheet: -1.93 (0.59), residues: 62 loop : -1.05 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.019 0.001 TYR B 491 PHE 0.013 0.001 PHE A 19 TRP 0.012 0.001 TRP B 520 HIS 0.002 0.001 HIS A 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6339) covalent geometry : angle 0.50562 / 0.26 ( 8841) hydrogen bonds : bond 0.03264 / 1.95 ( 178) hydrogen bonds : angle 4.11037 / 2.84 ( 430) metal coordination : bond 0.00986 / 0.61 ( 20) metal coordination : angle 1.83205 / 1.39 ( 17) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8154 (t) cc_final: 0.7878 (t) REVERT: B 58 MET cc_start: 0.9013 (mtp) cc_final: 0.8563 (mtp) REVERT: B 61 LYS cc_start: 0.8974 (mtpt) cc_final: 0.8643 (mtpp) REVERT: B 169 MET cc_start: 0.8757 (ttp) cc_final: 0.8436 (ptm) REVERT: B 185 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8666 (mt) REVERT: B 330 HIS cc_start: 0.7504 (m-70) cc_final: 0.7103 (m-70) REVERT: B 391 ARG cc_start: 0.8364 (ttm170) cc_final: 0.8026 (mtp180) REVERT: B 395 ASN cc_start: 0.8591 (p0) cc_final: 0.8302 (p0) REVERT: B 445 PHE cc_start: 0.8790 (p90) cc_final: 0.8452 (p90) outliers start: 20 outliers final: 17 residues processed: 106 average time/residue: 0.0479 time to fit residues: 7.0886 Evaluate side-chains 113 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 20.0000 chunk 50 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 57 optimal weight: 1.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.189961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.134623 restraints weight = 7604.011| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.58 r_work: 0.3277 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6359 Z= 0.120 Angle : 0.497 7.015 8858 Z= 0.251 Chirality : 0.038 0.149 1015 Planarity : 0.003 0.025 953 Dihedral : 9.868 173.517 1275 Min Nonbonded Distance : 1.124 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.25 % Allowed : 16.27 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.33), residues: 638 helix: -0.21 (0.46), residues: 143 sheet: -1.88 (0.60), residues: 62 loop : -0.97 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.010 0.001 TYR A 96 PHE 0.011 0.001 PHE B 133 TRP 0.017 0.001 TRP B 348 HIS 0.002 0.001 HIS B 424 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 6339) covalent geometry : angle 0.49174 / 0.25 ( 8841) hydrogen bonds : bond 0.03134 / 1.83 ( 178) hydrogen bonds : angle 4.14226 / 2.84 ( 430) metal coordination : bond 0.00761 / 0.48 ( 20) metal coordination : angle 1.67865 / 1.25 ( 17) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8105 (t) cc_final: 0.7835 (t) REVERT: B 58 MET cc_start: 0.9003 (mtp) cc_final: 0.8453 (mtp) REVERT: B 61 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8632 (mtpp) REVERT: B 169 MET cc_start: 0.8750 (ttp) cc_final: 0.8427 (ptm) REVERT: B 185 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8643 (mt) REVERT: B 330 HIS cc_start: 0.7263 (m-70) cc_final: 0.6771 (m-70) REVERT: B 377 PHE cc_start: 0.6934 (m-80) cc_final: 0.6601 (m-80) REVERT: B 391 ARG cc_start: 0.8339 (ttm170) cc_final: 0.7999 (mtp180) REVERT: B 395 ASN cc_start: 0.8554 (p0) cc_final: 0.8277 (p0) outliers start: 18 outliers final: 16 residues processed: 104 average time/residue: 0.0482 time to fit residues: 6.9668 Evaluate side-chains 110 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 30 optimal weight: 0.0980 chunk 7 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.0270 chunk 53 optimal weight: 0.0170 chunk 64 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.192000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136766 restraints weight = 7505.767| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.62 r_work: 0.3312 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6359 Z= 0.100 Angle : 0.500 9.469 8858 Z= 0.250 Chirality : 0.038 0.147 1015 Planarity : 0.003 0.025 953 Dihedral : 9.825 173.656 1275 Min Nonbonded Distance : 1.170 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.89 % Allowed : 16.46 % Favored : 80.65 % 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: -1.19 (0.33), residues: 638 helix: -0.14 (0.46), residues: 143 sheet: -1.75 (0.61), residues: 60 loop : -0.88 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.022 0.001 TYR A 96 PHE 0.010 0.001 PHE B 133 TRP 0.019 0.001 TRP B 520 HIS 0.004 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 6339) covalent geometry : angle 0.49549 / 0.25 ( 8841) hydrogen bonds : bond 0.03148 / 1.83 ( 178) hydrogen bonds : angle 4.02707 / 2.76 ( 430) metal coordination : bond 0.00585 / 0.36 ( 20) metal coordination : angle 1.66086 / 1.20 ( 17) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8095 (t) cc_final: 0.7824 (t) REVERT: B 58 MET cc_start: 0.8988 (mtp) cc_final: 0.8533 (mtp) REVERT: B 61 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8604 (mtpp) REVERT: B 154 TYR cc_start: 0.7681 (m-80) cc_final: 0.7402 (m-80) REVERT: B 169 MET cc_start: 0.8726 (ttp) cc_final: 0.8421 (ptm) REVERT: B 185 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 195 MET cc_start: 0.8880 (mtp) cc_final: 0.8644 (mtm) REVERT: B 330 HIS cc_start: 0.7379 (m-70) cc_final: 0.6970 (m-70) REVERT: B 377 PHE cc_start: 0.6844 (m-80) cc_final: 0.6393 (m-80) REVERT: B 391 ARG cc_start: 0.8368 (ttm170) cc_final: 0.8034 (mtp180) REVERT: B 395 ASN cc_start: 0.8491 (p0) cc_final: 0.8281 (p0) outliers start: 16 outliers final: 15 residues processed: 109 average time/residue: 0.0551 time to fit residues: 8.2613 Evaluate side-chains 110 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 32 LYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 241 MET Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 17 optimal weight: 0.0030 chunk 58 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 410 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.192442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135543 restraints weight = 7527.473| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.48 r_work: 0.3302 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6359 Z= 0.116 Angle : 0.502 8.706 8858 Z= 0.250 Chirality : 0.038 0.145 1015 Planarity : 0.003 0.028 953 Dihedral : 9.800 173.569 1275 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.89 % Allowed : 16.82 % Favored : 80.29 % 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: -1.16 (0.33), residues: 638 helix: -0.23 (0.44), residues: 149 sheet: -1.64 (0.62), residues: 62 loop : -0.83 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.015 0.001 TYR A 96 PHE 0.011 0.001 PHE B 133 TRP 0.019 0.001 TRP B 520 HIS 0.002 0.001 HIS B 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 6339) covalent geometry : angle 0.49642 / 0.25 ( 8841) hydrogen bonds : bond 0.03113 / 1.79 ( 178) hydrogen bonds : angle 4.09410 / 2.82 ( 430) metal coordination : bond 0.00898 / 0.56 ( 20) metal coordination : angle 1.82409 / 1.38 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1209.53 seconds wall clock time: 21 minutes 24.22 seconds (1284.22 seconds total)