Starting phenix.real_space_refine on Thu Jun 5 14:23:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0c_24103/06_2025/7n0c_24103.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0c_24103/06_2025/7n0c_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7n0c_24103/06_2025/7n0c_24103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0c_24103/06_2025/7n0c_24103.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0c_24103/06_2025/7n0c_24103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0c_24103/06_2025/7n0c_24103.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.58, per 1000 atoms: 0.92 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: 1.70 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 2.44 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: 2.56 Time building geometry restraints manager: 1.97 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: 3624 34.34 - 68.68: 129 68.68 - 103.02: 12 103.02 - 137.36: 0 137.36 - 171.70: 1 Dihedral angle restraints: 3766 sinusoidal: 1891 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 3763 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: 15.250 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 28.460 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 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 : 16.673 171.703 2562 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.002 TRP B 385 HIS 0.011 0.003 HIS B 257 PHE 0.040 0.003 PHE A 19 TYR 0.022 0.002 TYR A 76 ARG 0.005 0.001 ARG B 163 Details of bonding type rmsd hydrogen bonds : bond 0.18771 ( 178) hydrogen bonds : angle 7.65072 ( 430) metal coordination : bond 0.20625 ( 20) metal coordination : angle 13.43401 ( 17) covalent geometry : bond 0.00862 ( 6339) covalent geometry : angle 0.99601 ( 8841) *********************** 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 : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7961 (mmtp) REVERT: A 98 GLN cc_start: 0.8060 (mp-120) cc_final: 0.7752 (mm110) REVERT: A 114 ASN cc_start: 0.8736 (m-40) cc_final: 0.8522 (m110) REVERT: B 58 MET cc_start: 0.8765 (mtp) cc_final: 0.8335 (mtp) REVERT: B 169 MET cc_start: 0.8659 (ttp) cc_final: 0.7961 (tmm) REVERT: B 330 HIS cc_start: 0.7916 (m-70) cc_final: 0.6908 (m-70) REVERT: B 499 ASN cc_start: 0.7843 (m-40) cc_final: 0.7558 (m-40) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2201 time to fit residues: 29.9111 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 : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 0.0010 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 32 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4110 r_free = 0.4110 target = 0.178114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.121947 restraints weight = 7265.142| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.84 r_work: 0.3076 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1490 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= 0.128 Angle : 0.566 8.522 8858 Z= 0.284 Chirality : 0.040 0.148 1015 Planarity : 0.005 0.052 953 Dihedral : 16.317 172.780 1417 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.81 % Allowed : 10.49 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.29), residues: 638 helix: -1.92 (0.40), residues: 139 sheet: -3.00 (0.55), residues: 54 loop : -1.82 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 385 HIS 0.004 0.001 HIS B 283 PHE 0.014 0.001 PHE B 133 TYR 0.022 0.001 TYR B 370 ARG 0.004 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 178) hydrogen bonds : angle 5.01123 ( 430) metal coordination : bond 0.01143 ( 20) metal coordination : angle 4.19096 ( 17) covalent geometry : bond 0.00292 ( 6339) covalent geometry : angle 0.53643 ( 8841) *********************** 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: 10 poor density : 101 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8326 (t) cc_final: 0.8103 (t) REVERT: A 95 LYS cc_start: 0.7596 (mmtt) cc_final: 0.7270 (mmtp) REVERT: A 98 GLN cc_start: 0.8238 (mp-120) cc_final: 0.7819 (mm-40) REVERT: A 114 ASN cc_start: 0.8774 (m-40) cc_final: 0.8399 (m110) REVERT: B 58 MET cc_start: 0.8990 (mtp) cc_final: 0.8571 (mtp) REVERT: B 61 LYS cc_start: 0.9055 (mtpt) cc_final: 0.8726 (mtpp) REVERT: B 169 MET cc_start: 0.8801 (ttp) cc_final: 0.8503 (tmm) REVERT: B 185 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8533 (mt) REVERT: B 330 HIS cc_start: 0.7458 (m-70) cc_final: 0.6350 (m170) REVERT: B 384 PHE cc_start: 0.8993 (m-80) cc_final: 0.8736 (m-80) REVERT: B 391 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7604 (mtp180) REVERT: B 395 ASN cc_start: 0.8453 (p0) cc_final: 0.8116 (p0) REVERT: B 499 ASN cc_start: 0.7733 (m110) cc_final: 0.7441 (m-40) outliers start: 10 outliers final: 5 residues processed: 109 average time/residue: 0.1870 time to fit residues: 26.6767 Evaluate side-chains 95 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.0020 chunk 8 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4104 r_free = 0.4104 target = 0.177584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.123059 restraints weight = 7413.090| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.99 r_work: 0.3052 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6359 Z= 0.153 Angle : 0.544 6.494 8858 Z= 0.272 Chirality : 0.039 0.145 1015 Planarity : 0.005 0.072 953 Dihedral : 16.153 172.706 1417 Min Nonbonded Distance : 1.549 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.80 % Allowed : 10.85 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.31), residues: 638 helix: -1.33 (0.43), residues: 142 sheet: -2.75 (0.52), residues: 68 loop : -1.53 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 385 HIS 0.005 0.001 HIS B 257 PHE 0.015 0.001 PHE A 19 TYR 0.011 0.001 TYR B 370 ARG 0.004 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 178) hydrogen bonds : angle 4.63003 ( 430) metal coordination : bond 0.01289 ( 20) metal coordination : angle 3.06093 ( 17) covalent geometry : bond 0.00358 ( 6339) covalent geometry : angle 0.52733 ( 8841) *********************** 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 119 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8261 (t) cc_final: 0.7959 (t) REVERT: A 95 LYS cc_start: 0.7647 (mmtt) cc_final: 0.7341 (mmtp) REVERT: A 98 GLN cc_start: 0.8444 (mp-120) cc_final: 0.8080 (mm110) REVERT: A 114 ASN cc_start: 0.8748 (m-40) cc_final: 0.8371 (m110) REVERT: B 58 MET cc_start: 0.9080 (mtp) cc_final: 0.8673 (mtp) REVERT: B 61 LYS cc_start: 0.9115 (mtpt) cc_final: 0.8756 (mtpp) REVERT: B 169 MET cc_start: 0.8842 (ttp) cc_final: 0.8539 (ptm) REVERT: B 185 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8565 (mt) REVERT: B 330 HIS cc_start: 0.7664 (m-70) cc_final: 0.6884 (m170) REVERT: B 384 PHE cc_start: 0.9030 (m-80) cc_final: 0.8794 (m-80) REVERT: B 391 ARG cc_start: 0.8183 (ttm170) cc_final: 0.7752 (mtp180) REVERT: B 395 ASN cc_start: 0.8482 (p0) cc_final: 0.8047 (p0) REVERT: B 499 ASN cc_start: 0.7694 (m110) cc_final: 0.7459 (m110) outliers start: 21 outliers final: 13 residues processed: 111 average time/residue: 0.1963 time to fit residues: 30.1256 Evaluate side-chains 110 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 TRP Chi-restraints excluded: chain B residue 382 CYS Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 7 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.4980 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4108 r_free = 0.4108 target = 0.178070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121897 restraints weight = 7442.552| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.74 r_work: 0.3079 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2079 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= 0.140 Angle : 0.518 5.995 8858 Z= 0.262 Chirality : 0.039 0.140 1015 Planarity : 0.004 0.058 953 Dihedral : 16.048 172.879 1417 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.07 % Allowed : 13.02 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.05 (0.32), residues: 638 helix: -0.99 (0.45), residues: 143 sheet: -2.24 (0.60), residues: 60 loop : -1.41 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 PHE 0.016 0.002 PHE B 444 TYR 0.011 0.001 TYR B 447 ARG 0.002 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03203 ( 178) hydrogen bonds : angle 4.42170 ( 430) metal coordination : bond 0.00978 ( 20) metal coordination : angle 2.37932 ( 17) covalent geometry : bond 0.00327 ( 6339) covalent geometry : angle 0.50808 ( 8841) *********************** 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 112 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8137 (t) cc_final: 0.7846 (t) REVERT: A 95 LYS cc_start: 0.7621 (mmtt) cc_final: 0.7290 (mmtp) REVERT: A 114 ASN cc_start: 0.8716 (m-40) cc_final: 0.8349 (m110) REVERT: B 58 MET cc_start: 0.9061 (mtp) cc_final: 0.8670 (mtp) REVERT: B 61 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8714 (mtpp) REVERT: B 169 MET cc_start: 0.8795 (ttp) cc_final: 0.8496 (ptm) REVERT: B 185 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8566 (mt) REVERT: B 330 HIS cc_start: 0.7603 (m-70) cc_final: 0.6693 (m-70) REVERT: B 391 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7811 (mtp180) REVERT: B 395 ASN cc_start: 0.8493 (p0) cc_final: 0.8064 (p0) REVERT: B 398 VAL cc_start: 0.9011 (t) cc_final: 0.8602 (p) REVERT: B 445 PHE cc_start: 0.8965 (p90) cc_final: 0.8645 (p90) REVERT: B 499 ASN cc_start: 0.7721 (m110) cc_final: 0.7511 (m-40) outliers start: 17 outliers final: 15 residues processed: 103 average time/residue: 0.2070 time to fit residues: 29.1479 Evaluate side-chains 109 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 127 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 185 LEU 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 348 TRP Chi-restraints excluded: chain B residue 382 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.177846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.120062 restraints weight = 7408.619| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.57 r_work: 0.3102 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2293 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= 0.135 Angle : 0.505 5.222 8858 Z= 0.255 Chirality : 0.039 0.141 1015 Planarity : 0.004 0.071 953 Dihedral : 15.985 172.880 1417 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.52 % Allowed : 12.48 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.32), residues: 638 helix: -0.85 (0.45), residues: 143 sheet: -2.06 (0.59), residues: 60 loop : -1.28 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 PHE 0.013 0.001 PHE A 19 TYR 0.008 0.001 TYR B 420 ARG 0.004 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03194 ( 178) hydrogen bonds : angle 4.28613 ( 430) metal coordination : bond 0.00932 ( 20) metal coordination : angle 2.20788 ( 17) covalent geometry : bond 0.00315 ( 6339) covalent geometry : angle 0.49581 ( 8841) *********************** 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 122 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8105 (t) cc_final: 0.7849 (t) REVERT: A 95 LYS cc_start: 0.7583 (mmtt) cc_final: 0.7256 (mmtp) REVERT: A 114 ASN cc_start: 0.8710 (m-40) cc_final: 0.8329 (m110) REVERT: B 58 MET cc_start: 0.9057 (mtp) cc_final: 0.8663 (mtp) REVERT: B 61 LYS cc_start: 0.9071 (mtpt) cc_final: 0.8575 (mtpp) REVERT: B 169 MET cc_start: 0.8811 (ttp) cc_final: 0.8467 (ptm) REVERT: B 185 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8532 (mt) REVERT: B 330 HIS cc_start: 0.7373 (m-70) cc_final: 0.6664 (m170) REVERT: B 391 ARG cc_start: 0.8203 (ttm170) cc_final: 0.7762 (mtp180) REVERT: B 395 ASN cc_start: 0.8532 (p0) cc_final: 0.8097 (p0) REVERT: B 398 VAL cc_start: 0.9003 (t) cc_final: 0.8628 (p) REVERT: B 445 PHE cc_start: 0.8924 (p90) cc_final: 0.8606 (p90) REVERT: B 499 ASN cc_start: 0.7681 (m110) cc_final: 0.7460 (m-40) outliers start: 25 outliers final: 18 residues processed: 110 average time/residue: 0.1779 time to fit residues: 26.2857 Evaluate side-chains 113 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 94 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 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 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 13 optimal weight: 0.3980 chunk 58 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 42 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.189804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.134066 restraints weight = 7425.641| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.31 r_work: 0.3302 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6359 Z= 0.113 Angle : 0.491 7.183 8858 Z= 0.247 Chirality : 0.039 0.151 1015 Planarity : 0.004 0.059 953 Dihedral : 15.905 173.002 1417 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.80 % Allowed : 14.29 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.32), residues: 638 helix: -0.60 (0.46), residues: 144 sheet: -1.93 (0.59), residues: 60 loop : -1.16 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 PHE 0.018 0.001 PHE B 350 TYR 0.007 0.001 TYR B 420 ARG 0.005 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 178) hydrogen bonds : angle 4.21882 ( 430) metal coordination : bond 0.00717 ( 20) metal coordination : angle 1.87058 ( 17) covalent geometry : bond 0.00262 ( 6339) covalent geometry : angle 0.48492 ( 8841) *********************** 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 117 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8140 (t) cc_final: 0.7849 (t) REVERT: A 95 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7415 (mttm) REVERT: A 98 GLN cc_start: 0.7865 (mm-40) cc_final: 0.7055 (mm-40) REVERT: B 58 MET cc_start: 0.8995 (mtp) cc_final: 0.8467 (mtp) REVERT: B 61 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8598 (mtpp) REVERT: B 169 MET cc_start: 0.8680 (ttp) cc_final: 0.8404 (ptm) REVERT: B 330 HIS cc_start: 0.7215 (m-70) cc_final: 0.6881 (m-70) REVERT: B 391 ARG cc_start: 0.8333 (ttm170) cc_final: 0.8003 (mtp180) REVERT: B 395 ASN cc_start: 0.8607 (p0) cc_final: 0.8196 (p0) REVERT: B 398 VAL cc_start: 0.9041 (t) cc_final: 0.8739 (p) REVERT: B 445 PHE cc_start: 0.8911 (p90) cc_final: 0.8495 (p90) outliers start: 21 outliers final: 17 residues processed: 106 average time/residue: 0.1805 time to fit residues: 25.5829 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 : 0.554 ------------------------------------------------------------------------------- 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 223 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 334 ASN 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 45 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN B 334 ASN B 499 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.188125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133289 restraints weight = 7544.045| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.57 r_work: 0.3301 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6359 Z= 0.161 Angle : 0.520 6.064 8858 Z= 0.262 Chirality : 0.040 0.158 1015 Planarity : 0.004 0.064 953 Dihedral : 15.902 172.758 1417 Min Nonbonded Distance : 1.092 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.44 % Allowed : 15.37 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.32), residues: 638 helix: -0.58 (0.45), residues: 143 sheet: -2.00 (0.59), residues: 60 loop : -1.13 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 PHE 0.015 0.001 PHE A 19 TYR 0.008 0.001 TYR B 51 ARG 0.006 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03292 ( 178) hydrogen bonds : angle 4.28003 ( 430) metal coordination : bond 0.01166 ( 20) metal coordination : angle 2.05470 ( 17) covalent geometry : bond 0.00380 ( 6339) covalent geometry : angle 0.51241 ( 8841) *********************** 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 115 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8249 (t) cc_final: 0.7976 (t) REVERT: A 95 LYS cc_start: 0.8036 (mmtt) cc_final: 0.7758 (mmtp) REVERT: B 58 MET cc_start: 0.9136 (mtp) cc_final: 0.8717 (mtp) REVERT: B 61 LYS cc_start: 0.9025 (mtpt) cc_final: 0.8694 (mtpp) REVERT: B 169 MET cc_start: 0.8901 (ttp) cc_final: 0.8549 (ptm) REVERT: B 185 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8754 (mt) REVERT: B 330 HIS cc_start: 0.7447 (m-70) cc_final: 0.7127 (m-70) REVERT: B 391 ARG cc_start: 0.8575 (ttm170) cc_final: 0.8271 (mtp180) REVERT: B 395 ASN cc_start: 0.8663 (p0) cc_final: 0.8258 (p0) REVERT: B 398 VAL cc_start: 0.9106 (t) cc_final: 0.8842 (p) outliers start: 19 outliers final: 16 residues processed: 106 average time/residue: 0.1735 time to fit residues: 24.6913 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 : 0.558 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 348 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 334 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 = 0.4260 r_free = 0.4260 target = 0.189148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133455 restraints weight = 7494.581| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.41 r_work: 0.3261 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6359 Z= 0.132 Angle : 0.510 5.749 8858 Z= 0.258 Chirality : 0.040 0.198 1015 Planarity : 0.004 0.057 953 Dihedral : 15.876 172.846 1417 Min Nonbonded Distance : 1.108 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.25 % Allowed : 16.09 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.32), residues: 638 helix: -0.52 (0.45), residues: 142 sheet: -1.98 (0.59), residues: 60 loop : -1.08 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 PHE 0.018 0.001 PHE B 444 TYR 0.008 0.001 TYR A 96 ARG 0.006 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 178) hydrogen bonds : angle 4.28300 ( 430) metal coordination : bond 0.00890 ( 20) metal coordination : angle 1.89778 ( 17) covalent geometry : bond 0.00309 ( 6339) covalent geometry : angle 0.50392 ( 8841) *********************** 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 112 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8141 (t) cc_final: 0.7878 (t) REVERT: A 95 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7529 (mmtp) REVERT: B 58 MET cc_start: 0.9017 (mtp) cc_final: 0.8578 (mtp) REVERT: B 61 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8605 (mtpp) REVERT: B 169 MET cc_start: 0.8722 (ttp) cc_final: 0.8393 (ptm) REVERT: B 185 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8655 (mt) REVERT: B 330 HIS cc_start: 0.7312 (m-70) cc_final: 0.6957 (m-70) REVERT: B 391 ARG cc_start: 0.8393 (ttm170) cc_final: 0.8077 (mtp180) REVERT: B 395 ASN cc_start: 0.8621 (p0) cc_final: 0.8329 (p0) REVERT: B 398 VAL cc_start: 0.9050 (t) cc_final: 0.8730 (p) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.1774 time to fit residues: 24.5890 Evaluate side-chains 111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 287 VAL Chi-restraints excluded: chain B residue 341 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 44 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 38 optimal weight: 0.0050 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.191004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.135879 restraints weight = 7504.694| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.35 r_work: 0.3311 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2943 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= 0.108 Angle : 0.492 8.280 8858 Z= 0.247 Chirality : 0.039 0.195 1015 Planarity : 0.003 0.041 953 Dihedral : 15.768 173.155 1417 Min Nonbonded Distance : 1.132 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.62 % Allowed : 15.37 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.33), residues: 638 helix: -0.32 (0.45), residues: 143 sheet: -1.84 (0.60), residues: 60 loop : -0.96 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 520 HIS 0.004 0.001 HIS B 283 PHE 0.014 0.001 PHE B 350 TYR 0.010 0.001 TYR B 494 ARG 0.006 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03133 ( 178) hydrogen bonds : angle 4.18494 ( 430) metal coordination : bond 0.00635 ( 20) metal coordination : angle 1.71898 ( 17) covalent geometry : bond 0.00251 ( 6339) covalent geometry : angle 0.48693 ( 8841) *********************** 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 118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8094 (t) cc_final: 0.7838 (t) REVERT: A 95 LYS cc_start: 0.7872 (mmtt) cc_final: 0.7453 (mttm) REVERT: B 58 MET cc_start: 0.9009 (mtp) cc_final: 0.8472 (mtp) REVERT: B 61 LYS cc_start: 0.8895 (mtpt) cc_final: 0.8586 (mtpp) REVERT: B 154 TYR cc_start: 0.7714 (m-80) cc_final: 0.7439 (m-80) REVERT: B 169 MET cc_start: 0.8706 (ttp) cc_final: 0.8410 (ptm) REVERT: B 185 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8678 (mt) REVERT: B 330 HIS cc_start: 0.7532 (m-70) cc_final: 0.7148 (m-70) REVERT: B 349 LYS cc_start: 0.8234 (mtmt) cc_final: 0.7999 (mtpt) REVERT: B 391 ARG cc_start: 0.8401 (ttm170) cc_final: 0.8122 (mtp180) REVERT: B 395 ASN cc_start: 0.8549 (p0) cc_final: 0.8336 (p0) REVERT: B 398 VAL cc_start: 0.8999 (t) cc_final: 0.8706 (p) REVERT: B 445 PHE cc_start: 0.8819 (p90) cc_final: 0.8427 (p90) outliers start: 20 outliers final: 15 residues processed: 109 average time/residue: 0.1931 time to fit residues: 28.1305 Evaluate side-chains 109 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 341 VAL Chi-restraints excluded: chain B residue 348 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 67 optimal weight: 10.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 GLN ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.188631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.133386 restraints weight = 7510.524| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 2.55 r_work: 0.3248 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6359 Z= 0.171 Angle : 0.556 9.726 8858 Z= 0.278 Chirality : 0.041 0.203 1015 Planarity : 0.004 0.025 953 Dihedral : 15.789 172.758 1417 Min Nonbonded Distance : 1.093 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.07 % Allowed : 16.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.32), residues: 638 helix: -0.65 (0.43), residues: 149 sheet: -1.98 (0.59), residues: 60 loop : -0.94 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 520 HIS 0.004 0.001 HIS B 487 PHE 0.016 0.002 PHE A 19 TYR 0.015 0.001 TYR A 96 ARG 0.006 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 178) hydrogen bonds : angle 4.26055 ( 430) metal coordination : bond 0.01247 ( 20) metal coordination : angle 2.02256 ( 17) covalent geometry : bond 0.00403 ( 6339) covalent geometry : angle 0.54961 ( 8841) ********************** 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 111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 94 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8177 (t) cc_final: 0.7943 (t) REVERT: A 95 LYS cc_start: 0.7946 (mmtt) cc_final: 0.7648 (mmtp) REVERT: B 58 MET cc_start: 0.9069 (mtp) cc_final: 0.8562 (mtp) REVERT: B 61 LYS cc_start: 0.8966 (mtpt) cc_final: 0.8636 (mtpp) REVERT: B 169 MET cc_start: 0.8803 (ttp) cc_final: 0.8422 (ptm) REVERT: B 185 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8670 (mt) REVERT: B 330 HIS cc_start: 0.7452 (m-70) cc_final: 0.7073 (m-70) REVERT: B 391 ARG cc_start: 0.8423 (ttm170) cc_final: 0.8062 (mtp180) REVERT: B 395 ASN cc_start: 0.8647 (p0) cc_final: 0.8427 (p0) REVERT: B 398 VAL cc_start: 0.9073 (t) cc_final: 0.8752 (p) REVERT: B 445 PHE cc_start: 0.8855 (p90) cc_final: 0.8423 (p90) outliers start: 17 outliers final: 15 residues processed: 104 average time/residue: 0.1661 time to fit residues: 23.6545 Evaluate side-chains 105 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 89 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 341 VAL Chi-restraints excluded: chain B residue 348 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 30.0000 chunk 29 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 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 = 0.4087 r_free = 0.4087 target = 0.176761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.121588 restraints weight = 7540.450| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.00 r_work: 0.3027 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 6359 Z= 0.223 Angle : 0.603 9.437 8858 Z= 0.302 Chirality : 0.042 0.215 1015 Planarity : 0.004 0.026 953 Dihedral : 15.868 172.052 1417 Min Nonbonded Distance : 1.055 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.33), residues: 638 helix: -0.44 (0.46), residues: 137 sheet: -2.39 (0.54), residues: 69 loop : -0.94 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 520 HIS 0.003 0.001 HIS B 95 PHE 0.021 0.002 PHE A 19 TYR 0.021 0.002 TYR B 491 ARG 0.006 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 178) hydrogen bonds : angle 4.41174 ( 430) metal coordination : bond 0.01719 ( 20) metal coordination : angle 2.44987 ( 17) covalent geometry : bond 0.00525 ( 6339) covalent geometry : angle 0.59352 ( 8841) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3836.30 seconds wall clock time: 67 minutes 56.66 seconds (4076.66 seconds total)