Starting phenix.real_space_refine on Fri Sep 11 01:04:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7n0c_24103/09_2026/7n0c_24103.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0c_24103/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7n0c_24103/09_2026/7n0c_24103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0c_24103/09_2026/7n0c_24103.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0c_24103/09_2026/7n0c_24103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0c_24103/09_2026/7n0c_24103.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7n0c_24103/09_2026/7n0c_24103.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7n0c_24103/09_2026/7n0c_24103.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 1.46, per 1000 atoms: 0.24 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: 0.56 Conformation dependent library (CDL) restraints added in 436.9 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: 0.64 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: 1.18 Time building geometry restraints manager: 0.77 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: 8131 1.82 - 3.63: 599 3.63 - 5.45: 86 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 - 15.31: 3147 15.31 - 30.63: 325 30.63 - 45.94: 91 45.94 - 61.26: 56 61.26 - 76.57: 5 Dihedral angle restraints: 3624 sinusoidal: 1749 harmonic: 1875 Sorted by residual: dihedral pdb=" C4' U T 6 " pdb=" C3' U T 6 " pdb=" C2' U T 6 " pdb=" C1' U T 6 " ideal model delta sinusoidal sigma weight residual 36.35 -33.93 70.27 1 3.10e+00 1.04e-01 6.62e+02 dihedral pdb=" O4' U T 6 " pdb=" C4' U T 6 " pdb=" C3' U T 6 " pdb=" C2' U T 6 " ideal model delta sinusoidal sigma weight residual -35.15 23.64 -58.79 1 4.00e+00 6.25e-02 2.89e+02 dihedral pdb=" O4' U T 6 " pdb=" C2' U T 6 " pdb=" C1' U T 6 " pdb=" C3' U T 6 " ideal model delta sinusoidal sigma weight residual 25.59 -33.50 59.10 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 3621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 715 0.054 - 0.108: 192 0.108 - 0.162: 44 0.162 - 0.216: 22 0.216 - 0.270: 42 Chirality restraints: 1015 Sorted by residual: chirality pdb=" C2' U T 6 " pdb=" C3' U T 6 " pdb=" O2' U T 6 " pdb=" C1' U T 6 " both_signs ideal model delta sigma weight residual False -2.79 -2.52 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" P U T 8 " pdb=" OP1 U T 8 " pdb=" OP2 U T 8 " pdb=" O5' U T 8 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" P U T 13 " pdb=" OP1 U T 13 " pdb=" OP2 U T 13 " pdb=" O5' U T 13 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.65e+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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.040 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- 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= 0.558 Angle : 1.199 25.154 8858 Z= 0.630 Chirality : 0.073 0.270 1015 Planarity : 0.007 0.059 953 Dihedral : 14.950 76.574 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 0.00867 / 0.43 ( 6339) covalent geometry : angle 1.04565 / 0.62 ( 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 : 0.203 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: 0.0920 time to fit residues: 12.5892 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 : 0.210 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.4102 r_free = 0.4102 target = 0.177300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122347 restraints weight = 7456.272| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 3.06 r_work: 0.3035 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6359 Z= 0.174 Angle : 0.701 12.683 8858 Z= 0.322 Chirality : 0.053 0.688 1015 Planarity : 0.005 0.059 953 Dihedral : 11.948 72.017 1275 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.17 % Allowed : 10.49 % Favored : 87.34 % 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: -2.96 (0.29), residues: 638 helix: -1.99 (0.39), residues: 139 sheet: -3.10 (0.49), residues: 68 loop : -1.83 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 78 TYR 0.023 0.001 TYR B 370 PHE 0.016 0.002 PHE A 19 TRP 0.009 0.001 TRP B 385 HIS 0.005 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 ( 6339) covalent geometry : angle 0.67402 / 0.32 ( 8841) hydrogen bonds : bond 0.04000 / 2.58 ( 178) hydrogen bonds : angle 5.04534 / 3.52 ( 430) metal coordination : bond 0.01591 / 0.85 ( 20) metal coordination : angle 4.45098 / 3.51 ( 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 : 0.197 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8374 (t) cc_final: 0.8167 (t) REVERT: A 95 LYS cc_start: 0.7686 (mmtt) cc_final: 0.7482 (mmtp) REVERT: A 98 GLN cc_start: 0.8291 (mp-120) cc_final: 0.7850 (mm-40) REVERT: A 114 ASN cc_start: 0.8828 (m-40) cc_final: 0.8433 (m110) REVERT: B 58 MET cc_start: 0.9049 (mtp) cc_final: 0.8629 (mtp) REVERT: B 61 LYS cc_start: 0.9134 (mtpt) cc_final: 0.8792 (mtpp) REVERT: B 169 MET cc_start: 0.8851 (ttp) cc_final: 0.8513 (tmm) REVERT: B 185 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8598 (mt) REVERT: B 330 HIS cc_start: 0.7542 (m-70) cc_final: 0.6425 (m170) REVERT: B 384 PHE cc_start: 0.9054 (m-80) cc_final: 0.8827 (m-80) REVERT: B 391 ARG cc_start: 0.8248 (ttm170) cc_final: 0.7810 (mtp180) REVERT: B 395 ASN cc_start: 0.8469 (p0) cc_final: 0.8134 (p0) REVERT: B 499 ASN cc_start: 0.7754 (m110) cc_final: 0.7457 (m-40) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.0838 time to fit residues: 11.9655 Evaluate side-chains 100 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.194 ------------------------------------------------------------------------------- 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: 1.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4117 r_free = 0.4117 target = 0.178618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.120866 restraints weight = 7344.666| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.58 r_work: 0.3121 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2058 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= 0.128 Angle : 0.610 6.724 8858 Z= 0.280 Chirality : 0.046 0.228 1015 Planarity : 0.004 0.034 953 Dihedral : 11.583 71.615 1275 Min Nonbonded Distance : 1.479 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.16 % Allowed : 10.67 % 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: -2.21 (0.31), residues: 638 helix: -1.10 (0.45), residues: 137 sheet: -2.50 (0.56), residues: 67 loop : -1.46 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 404 TYR 0.010 0.001 TYR B 370 PHE 0.012 0.001 PHE B 133 TRP 0.007 0.001 TRP B 520 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6339) covalent geometry : angle 0.59913 / 0.28 ( 8841) hydrogen bonds : bond 0.03314 / 2.07 ( 178) hydrogen bonds : angle 4.56092 / 3.15 ( 430) metal coordination : bond 0.00923 / 0.55 ( 20) metal coordination : angle 2.68814 / 2.10 ( 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 123 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 100 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8160 (t) cc_final: 0.7842 (t) REVERT: A 95 LYS cc_start: 0.7531 (mmtt) cc_final: 0.7200 (mmtp) REVERT: A 114 ASN cc_start: 0.8733 (m-40) cc_final: 0.8424 (m110) REVERT: A 126 TYR cc_start: 0.6637 (m-80) cc_final: 0.6433 (m-80) REVERT: B 58 MET cc_start: 0.9017 (mtp) cc_final: 0.8594 (mtp) REVERT: B 61 LYS cc_start: 0.9022 (mtpt) cc_final: 0.8623 (mtpp) REVERT: B 169 MET cc_start: 0.8779 (ttp) cc_final: 0.8511 (ptm) REVERT: B 330 HIS cc_start: 0.7582 (m-70) cc_final: 0.6825 (m170) REVERT: B 384 PHE cc_start: 0.8985 (m-80) cc_final: 0.8777 (m-80) REVERT: B 391 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7676 (mtp180) REVERT: B 395 ASN cc_start: 0.8494 (p0) cc_final: 0.8051 (p0) REVERT: B 398 VAL cc_start: 0.9084 (t) cc_final: 0.8696 (p) REVERT: B 499 ASN cc_start: 0.7727 (m110) cc_final: 0.7493 (m110) outliers start: 23 outliers final: 14 residues processed: 111 average time/residue: 0.0747 time to fit residues: 11.2664 Evaluate side-chains 108 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.195 ------------------------------------------------------------------------------- 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 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 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 59 optimal weight: 8.9990 chunk 3 optimal weight: 0.0270 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.0060 chunk 6 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 overall best weight: 0.5254 ------------------------------------------------------------------------------- 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 = 0.4121 r_free = 0.4121 target = 0.180124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120218 restraints weight = 7403.485| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 2.65 r_work: 0.3095 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2320 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= 0.119 Angle : 0.591 7.102 8858 Z= 0.273 Chirality : 0.046 0.239 1015 Planarity : 0.004 0.032 953 Dihedral : 11.139 72.029 1275 Min Nonbonded Distance : 1.266 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.89 % Allowed : 12.48 % Favored : 84.63 % 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: -1.98 (0.32), residues: 638 helix: -1.02 (0.44), residues: 150 sheet: -2.18 (0.60), residues: 60 loop : -1.32 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 404 TYR 0.008 0.001 TYR B 370 PHE 0.018 0.001 PHE B 444 TRP 0.007 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 6339) covalent geometry : angle 0.58450 / 0.27 ( 8841) hydrogen bonds : bond 0.03238 / 2.01 ( 178) hydrogen bonds : angle 4.28878 / 2.95 ( 430) metal coordination : bond 0.00710 / 0.44 ( 20) metal coordination : angle 2.03958 / 1.58 ( 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 114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.205 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8164 (t) cc_final: 0.7887 (t) REVERT: A 114 ASN cc_start: 0.8716 (m-40) cc_final: 0.8395 (m110) REVERT: B 58 MET cc_start: 0.9030 (mtp) cc_final: 0.8610 (mtp) REVERT: B 61 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8566 (mtpp) REVERT: B 169 MET cc_start: 0.8800 (ttp) cc_final: 0.8498 (ptm) REVERT: B 185 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8513 (mt) REVERT: B 330 HIS cc_start: 0.7667 (m-70) cc_final: 0.6773 (m-70) REVERT: B 334 ASN cc_start: 0.8349 (t0) cc_final: 0.8091 (p0) REVERT: B 391 ARG cc_start: 0.8189 (ttm170) cc_final: 0.7798 (mtp180) REVERT: B 395 ASN cc_start: 0.8517 (p0) cc_final: 0.8097 (p0) REVERT: B 398 VAL cc_start: 0.9072 (t) cc_final: 0.8672 (p) REVERT: B 445 PHE cc_start: 0.8917 (p90) cc_final: 0.8602 (p90) REVERT: B 499 ASN cc_start: 0.7691 (m110) cc_final: 0.7474 (m-40) outliers start: 16 outliers final: 13 residues processed: 106 average time/residue: 0.0711 time to fit residues: 10.3958 Evaluate side-chains 104 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.4107 r_free = 0.4107 target = 0.178806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.122164 restraints weight = 7570.558| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.94 r_work: 0.3059 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2384 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= 0.155 Angle : 0.601 7.085 8858 Z= 0.278 Chirality : 0.046 0.230 1015 Planarity : 0.004 0.026 953 Dihedral : 10.997 71.824 1275 Min Nonbonded Distance : 1.110 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.44 % Allowed : 13.02 % Favored : 83.54 % 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: -1.89 (0.32), residues: 638 helix: -0.91 (0.45), residues: 143 sheet: -2.09 (0.60), residues: 60 loop : -1.28 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 78 TYR 0.008 0.001 TYR B 420 PHE 0.014 0.001 PHE A 19 TRP 0.007 0.001 TRP B 520 HIS 0.003 0.001 HIS B 283 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 6339) covalent geometry : angle 0.59445 / 0.28 ( 8841) hydrogen bonds : bond 0.03328 / 2.05 ( 178) hydrogen bonds : angle 4.30897 / 2.98 ( 430) metal coordination : bond 0.01160 / 0.72 ( 20) metal coordination : angle 2.14915 / 1.65 ( 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 114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8047 (t) cc_final: 0.7767 (t) REVERT: A 114 ASN cc_start: 0.8765 (m-40) cc_final: 0.8414 (m110) REVERT: B 58 MET cc_start: 0.9046 (mtp) cc_final: 0.8638 (mtp) REVERT: B 61 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8601 (mtpp) REVERT: B 169 MET cc_start: 0.8833 (ttp) cc_final: 0.8530 (ptm) REVERT: B 185 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8404 (mt) REVERT: B 330 HIS cc_start: 0.7498 (m-70) cc_final: 0.6542 (m-70) REVERT: B 352 ASP cc_start: 0.7007 (t0) cc_final: 0.6750 (t70) REVERT: B 373 HIS cc_start: 0.8410 (m90) cc_final: 0.8005 (m90) REVERT: B 391 ARG cc_start: 0.8179 (ttm170) cc_final: 0.7707 (mtp180) REVERT: B 395 ASN cc_start: 0.8557 (p0) cc_final: 0.8101 (p0) REVERT: B 398 VAL cc_start: 0.9073 (t) cc_final: 0.8656 (p) REVERT: B 445 PHE cc_start: 0.8881 (p90) cc_final: 0.8618 (p90) outliers start: 19 outliers final: 15 residues processed: 107 average time/residue: 0.0597 time to fit residues: 8.8234 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 : 0.192 ------------------------------------------------------------------------------- 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 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 287 VAL Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 348 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 42 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 10 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.5582 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.189818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132731 restraints weight = 7456.872| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.62 r_work: 0.3266 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2625 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= 0.120 Angle : 0.575 7.350 8858 Z= 0.265 Chirality : 0.046 0.221 1015 Planarity : 0.003 0.025 953 Dihedral : 10.852 71.578 1275 Min Nonbonded Distance : 1.124 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.44 % Allowed : 14.83 % 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: -1.68 (0.32), residues: 638 helix: -0.66 (0.46), residues: 144 sheet: -1.91 (0.60), residues: 60 loop : -1.19 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.007 0.001 TYR B 420 PHE 0.017 0.001 PHE B 444 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 0.00278 / 0.12 ( 6339) covalent geometry : angle 0.57063 / 0.26 ( 8841) hydrogen bonds : bond 0.03203 / 1.96 ( 178) hydrogen bonds : angle 4.19627 / 2.89 ( 430) metal coordination : bond 0.00705 / 0.43 ( 20) metal coordination : angle 1.78761 / 1.36 ( 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 118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8184 (t) cc_final: 0.7880 (t) REVERT: B 58 MET cc_start: 0.8995 (mtp) cc_final: 0.8438 (mtp) REVERT: B 61 LYS cc_start: 0.9032 (mtpt) cc_final: 0.8699 (mtpp) REVERT: B 169 MET cc_start: 0.8731 (ttp) cc_final: 0.8437 (ptm) REVERT: B 185 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8613 (mt) REVERT: B 195 MET cc_start: 0.8781 (mtp) cc_final: 0.8569 (mtm) REVERT: B 315 MET cc_start: 0.8622 (tmm) cc_final: 0.8414 (tmm) REVERT: B 330 HIS cc_start: 0.7589 (m-70) cc_final: 0.6798 (m-70) REVERT: B 352 ASP cc_start: 0.7153 (t0) cc_final: 0.6905 (t70) REVERT: B 391 ARG cc_start: 0.8356 (ttm170) cc_final: 0.8027 (mtp180) REVERT: B 395 ASN cc_start: 0.8613 (p0) cc_final: 0.8313 (p0) REVERT: B 398 VAL cc_start: 0.9113 (t) cc_final: 0.8761 (p) REVERT: B 445 PHE cc_start: 0.8912 (p90) cc_final: 0.8554 (p90) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 0.0641 time to fit residues: 9.7916 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 : 0.193 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 27 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4253 r_free = 0.4253 target = 0.188649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.131606 restraints weight = 7536.120| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 2.45 r_work: 0.3252 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6359 Z= 0.152 Angle : 0.605 7.226 8858 Z= 0.280 Chirality : 0.046 0.222 1015 Planarity : 0.003 0.025 953 Dihedral : 10.779 71.689 1275 Min Nonbonded Distance : 1.101 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.98 % Allowed : 15.73 % 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: -1.66 (0.32), residues: 638 helix: -0.67 (0.45), residues: 143 sheet: -1.85 (0.59), residues: 60 loop : -1.17 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.011 0.001 TYR B 260 PHE 0.017 0.001 PHE B 350 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 0.00355 / 0.15 ( 6339) covalent geometry : angle 0.59908 / 0.28 ( 8841) hydrogen bonds : bond 0.03376 / 2.05 ( 178) hydrogen bonds : angle 4.18729 / 2.90 ( 430) metal coordination : bond 0.01022 / 0.63 ( 20) metal coordination : angle 1.94361 / 1.48 ( 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 117 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8201 (t) cc_final: 0.7918 (t) REVERT: B 58 MET cc_start: 0.9025 (mtp) cc_final: 0.8533 (mtp) REVERT: B 61 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8680 (mtpp) REVERT: B 169 MET cc_start: 0.8750 (ttp) cc_final: 0.8438 (ptm) REVERT: B 185 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8633 (mt) REVERT: B 330 HIS cc_start: 0.7481 (m-70) cc_final: 0.6990 (m-70) REVERT: B 391 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8039 (mtp180) REVERT: B 395 ASN cc_start: 0.8602 (p0) cc_final: 0.8318 (p0) REVERT: B 398 VAL cc_start: 0.9066 (t) cc_final: 0.8699 (p) REVERT: B 445 PHE cc_start: 0.8911 (p90) cc_final: 0.8617 (p90) outliers start: 22 outliers final: 16 residues processed: 108 average time/residue: 0.0668 time to fit residues: 10.0198 Evaluate side-chains 114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain B residue 122 THR 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 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: 4.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4257 r_free = 0.4257 target = 0.189052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132125 restraints weight = 7469.207| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.36 r_work: 0.3265 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2790 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= 0.145 Angle : 0.598 7.206 8858 Z= 0.276 Chirality : 0.046 0.219 1015 Planarity : 0.003 0.026 953 Dihedral : 10.720 71.859 1275 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.07 % Allowed : 16.82 % Favored : 80.11 % 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: -1.53 (0.32), residues: 638 helix: -0.51 (0.45), residues: 137 sheet: -2.01 (0.56), residues: 67 loop : -1.03 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.010 0.001 TYR B 260 PHE 0.017 0.001 PHE B 350 TRP 0.015 0.001 TRP B 520 HIS 0.002 0.001 HIS B 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.14 ( 6339) covalent geometry : angle 0.59310 / 0.28 ( 8841) hydrogen bonds : bond 0.03372 / 2.03 ( 178) hydrogen bonds : angle 4.25480 / 2.94 ( 430) metal coordination : bond 0.00991 / 0.62 ( 20) metal coordination : angle 1.91546 / 1.45 ( 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 114 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8170 (t) cc_final: 0.7892 (t) REVERT: B 58 MET cc_start: 0.9019 (mtp) cc_final: 0.8539 (mtp) REVERT: B 61 LYS cc_start: 0.9016 (mtpt) cc_final: 0.8692 (mtpp) REVERT: B 169 MET cc_start: 0.8748 (ttp) cc_final: 0.8429 (ptm) REVERT: B 185 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8621 (mt) REVERT: B 330 HIS cc_start: 0.7331 (m-70) cc_final: 0.7055 (m-70) REVERT: B 391 ARG cc_start: 0.8394 (ttm170) cc_final: 0.8050 (mtp180) REVERT: B 395 ASN cc_start: 0.8588 (p0) cc_final: 0.8310 (p0) REVERT: B 398 VAL cc_start: 0.9070 (t) cc_final: 0.8701 (p) REVERT: B 445 PHE cc_start: 0.8900 (p90) cc_final: 0.8487 (p90) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.0695 time to fit residues: 10.2077 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 : 0.198 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain B residue 122 THR 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 348 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 66 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 22 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 60 optimal weight: 40.0000 chunk 39 optimal weight: 0.4980 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.190739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133332 restraints weight = 7655.222| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.48 r_work: 0.3259 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6359 Z= 0.150 Angle : 0.619 8.019 8858 Z= 0.285 Chirality : 0.046 0.217 1015 Planarity : 0.003 0.026 953 Dihedral : 10.656 72.059 1275 Min Nonbonded Distance : 1.097 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.44 % Allowed : 16.46 % Favored : 80.11 % 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: -0.47 (0.45), residues: 137 sheet: -2.03 (0.55), residues: 67 loop : -0.99 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.019 0.001 TYR A 96 PHE 0.017 0.001 PHE B 350 TRP 0.016 0.001 TRP B 520 HIS 0.004 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 6339) covalent geometry : angle 0.61351 / 0.28 ( 8841) hydrogen bonds : bond 0.03453 / 2.06 ( 178) hydrogen bonds : angle 4.25236 / 2.94 ( 430) metal coordination : bond 0.01132 / 0.71 ( 20) metal coordination : angle 2.01223 / 1.47 ( 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 116 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8172 (t) cc_final: 0.7899 (t) REVERT: B 58 MET cc_start: 0.9019 (mtp) cc_final: 0.8528 (mtp) REVERT: B 61 LYS cc_start: 0.9027 (mtpt) cc_final: 0.8696 (mtpp) REVERT: B 169 MET cc_start: 0.8775 (ttp) cc_final: 0.8431 (ptm) REVERT: B 185 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8616 (mt) REVERT: B 315 MET cc_start: 0.8199 (tmm) cc_final: 0.7704 (tmm) REVERT: B 330 HIS cc_start: 0.7289 (m-70) cc_final: 0.6843 (m-70) REVERT: B 377 PHE cc_start: 0.6984 (m-80) cc_final: 0.6732 (m-80) REVERT: B 391 ARG cc_start: 0.8430 (ttm170) cc_final: 0.8106 (mtp180) REVERT: B 395 ASN cc_start: 0.8599 (p0) cc_final: 0.8309 (p0) REVERT: B 398 VAL cc_start: 0.9065 (t) cc_final: 0.8690 (p) REVERT: B 445 PHE cc_start: 0.8859 (p90) cc_final: 0.8419 (p90) outliers start: 19 outliers final: 17 residues processed: 105 average time/residue: 0.0639 time to fit residues: 9.3206 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 : 0.211 ------------------------------------------------------------------------------- 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 105 LEU Chi-restraints excluded: chain B residue 122 THR 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 Chi-restraints excluded: chain B residue 382 CYS 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: 0.8980 chunk 50 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 53 optimal weight: 0.0000 chunk 64 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 31 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.4584 ------------------------------------------------------------------------------- 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 = 0.4288 r_free = 0.4288 target = 0.192346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133987 restraints weight = 7545.574| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.47 r_work: 0.3284 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.3022 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= 0.116 Angle : 0.601 9.764 8858 Z= 0.276 Chirality : 0.046 0.212 1015 Planarity : 0.003 0.025 953 Dihedral : 10.610 72.068 1275 Min Nonbonded Distance : 1.138 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.07 % Allowed : 17.54 % Favored : 79.39 % 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: -1.34 (0.33), residues: 638 helix: -0.34 (0.45), residues: 137 sheet: -1.97 (0.57), residues: 67 loop : -0.89 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.021 0.001 TYR B 447 PHE 0.017 0.001 PHE B 350 TRP 0.020 0.001 TRP B 520 HIS 0.001 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 6339) covalent geometry : angle 0.59649 / 0.28 ( 8841) hydrogen bonds : bond 0.03332 / 1.99 ( 178) hydrogen bonds : angle 4.24090 / 2.91 ( 430) metal coordination : bond 0.00876 / 0.54 ( 20) metal coordination : angle 1.83622 / 1.34 ( 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 113 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8124 (t) cc_final: 0.7844 (t) REVERT: B 58 MET cc_start: 0.8993 (mtp) cc_final: 0.8411 (mtp) REVERT: B 61 LYS cc_start: 0.9005 (mtpt) cc_final: 0.8681 (mtpp) REVERT: B 154 TYR cc_start: 0.7732 (m-80) cc_final: 0.7432 (m-80) REVERT: B 169 MET cc_start: 0.8743 (ttp) cc_final: 0.8420 (ptm) REVERT: B 185 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8633 (mt) REVERT: B 330 HIS cc_start: 0.7203 (m-70) cc_final: 0.6767 (m-70) REVERT: B 377 PHE cc_start: 0.7025 (m-80) cc_final: 0.6769 (m-80) REVERT: B 391 ARG cc_start: 0.8389 (ttm170) cc_final: 0.8059 (mtp180) REVERT: B 395 ASN cc_start: 0.8528 (p0) cc_final: 0.8310 (p0) REVERT: B 398 VAL cc_start: 0.9094 (t) cc_final: 0.8718 (p) REVERT: B 445 PHE cc_start: 0.8822 (p90) cc_final: 0.8500 (p90) outliers start: 17 outliers final: 16 residues processed: 105 average time/residue: 0.0696 time to fit residues: 10.0542 Evaluate side-chains 109 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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 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 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 22 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 44 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.191328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.132134 restraints weight = 7542.471| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.46 r_work: 0.3267 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6359 Z= 0.142 Angle : 0.624 12.169 8858 Z= 0.286 Chirality : 0.047 0.214 1015 Planarity : 0.003 0.025 953 Dihedral : 10.583 72.162 1275 Min Nonbonded Distance : 1.098 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.25 % Allowed : 17.36 % Favored : 79.39 % 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: -1.31 (0.33), residues: 638 helix: -0.43 (0.45), residues: 137 sheet: -1.95 (0.57), residues: 67 loop : -0.83 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 78 TYR 0.021 0.001 TYR A 96 PHE 0.016 0.001 PHE B 350 TRP 0.022 0.001 TRP B 520 HIS 0.002 0.001 HIS B 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 6339) covalent geometry : angle 0.61815 / 0.29 ( 8841) hydrogen bonds : bond 0.03522 / 2.09 ( 178) hydrogen bonds : angle 4.38938 / 3.01 ( 430) metal coordination : bond 0.01173 / 0.73 ( 20) metal coordination : angle 2.07946 / 1.56 ( 17) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1583.80 seconds wall clock time: 27 minutes 55.22 seconds (1675.22 seconds total)