Starting phenix.real_space_refine on Tue Mar 11 16:51:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n0c_24103/03_2025/7n0c_24103.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n0c_24103/03_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_24103/03_2025/7n0c_24103.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n0c_24103/03_2025/7n0c_24103.map" model { file = "/net/cci-nas-00/data/ceres_data/7n0c_24103/03_2025/7n0c_24103.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n0c_24103/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.17, per 1000 atoms: 0.68 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: 1.42 Conformation dependent library (CDL) restraints added in 720.0 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: 2.03 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: 2.06 Time building geometry restraints manager: 1.70 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: 0.810 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.640 Find NCS groups from input model: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- 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 : 0.009 0.082 6339 Z= 0.571 Angle : 0.996 9.085 8841 Z= 0.611 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 *********************** 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 : 0.568 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: 0.2169 time to fit residues: 29.3861 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 : 0.626 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.5586 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.177998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121725 restraints weight = 7259.561| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.85 r_work: 0.3072 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6339 Z= 0.193 Angle : 0.541 5.751 8841 Z= 0.284 Chirality : 0.039 0.148 1015 Planarity : 0.005 0.052 953 Dihedral : 16.332 172.709 1417 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.63 % Allowed : 10.85 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.85 (0.29), residues: 638 helix: -1.96 (0.39), residues: 139 sheet: -2.75 (0.60), residues: 48 loop : -1.87 (0.26), residues: 451 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 0.013 0.001 PHE B 133 TYR 0.023 0.001 TYR B 370 ARG 0.005 0.000 ARG A 78 *********************** 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 112 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8349 (t) cc_final: 0.8131 (t) REVERT: A 95 LYS cc_start: 0.7622 (mmtt) cc_final: 0.7289 (mmtp) REVERT: A 98 GLN cc_start: 0.8244 (mp-120) cc_final: 0.7827 (mm-40) REVERT: A 114 ASN cc_start: 0.8778 (m-40) cc_final: 0.8411 (m110) REVERT: B 58 MET cc_start: 0.8994 (mtp) cc_final: 0.8575 (mtp) REVERT: B 61 LYS cc_start: 0.9115 (mtpt) cc_final: 0.8787 (mtpp) REVERT: B 169 MET cc_start: 0.8805 (ttp) cc_final: 0.8506 (tmm) REVERT: B 330 HIS cc_start: 0.7447 (m-70) cc_final: 0.6330 (m170) REVERT: B 368 TYR cc_start: 0.8066 (t80) cc_final: 0.7852 (t80) REVERT: B 384 PHE cc_start: 0.8997 (m-80) cc_final: 0.8741 (m-80) REVERT: B 391 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7610 (mtp180) REVERT: B 395 ASN cc_start: 0.8456 (p0) cc_final: 0.8119 (p0) REVERT: B 499 ASN cc_start: 0.7748 (m110) cc_final: 0.7461 (m-40) outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 0.1945 time to fit residues: 28.2165 Evaluate side-chains 95 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 223 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 47 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 8 optimal weight: 0.1980 chunk 64 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.178726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.124030 restraints weight = 7403.249| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.08 r_work: 0.3069 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6339 Z= 0.197 Angle : 0.514 6.485 8841 Z= 0.264 Chirality : 0.039 0.145 1015 Planarity : 0.004 0.065 953 Dihedral : 16.128 172.862 1417 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 3.25 % Allowed : 10.85 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.32 (0.31), residues: 638 helix: -1.31 (0.43), residues: 142 sheet: -2.37 (0.58), residues: 60 loop : -1.56 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 520 HIS 0.004 0.001 HIS B 257 PHE 0.012 0.001 PHE A 19 TYR 0.009 0.001 TYR B 370 ARG 0.003 0.000 ARG B 404 *********************** 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 118 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8158 (t) cc_final: 0.7909 (t) REVERT: A 40 ASN cc_start: 0.8855 (t0) cc_final: 0.8496 (t0) REVERT: A 95 LYS cc_start: 0.7510 (mmtt) cc_final: 0.7195 (mmtp) REVERT: A 98 GLN cc_start: 0.8437 (mp-120) cc_final: 0.8076 (mm110) REVERT: A 114 ASN cc_start: 0.8746 (m-40) cc_final: 0.8319 (m110) REVERT: B 58 MET cc_start: 0.9049 (mtp) cc_final: 0.8647 (mtp) REVERT: B 61 LYS cc_start: 0.9037 (mtpt) cc_final: 0.8658 (mtpp) REVERT: B 169 MET cc_start: 0.8821 (ttp) cc_final: 0.8524 (ptm) REVERT: B 185 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8453 (mt) REVERT: B 330 HIS cc_start: 0.7532 (m-70) cc_final: 0.6733 (m170) REVERT: B 384 PHE cc_start: 0.8992 (m-80) cc_final: 0.8751 (m-80) REVERT: B 391 ARG cc_start: 0.8200 (ttm170) cc_final: 0.7632 (mtp180) REVERT: B 395 ASN cc_start: 0.8492 (p0) cc_final: 0.8054 (p0) REVERT: B 499 ASN cc_start: 0.7686 (m110) cc_final: 0.7459 (m110) outliers start: 18 outliers final: 12 residues processed: 110 average time/residue: 0.1844 time to fit residues: 27.7070 Evaluate side-chains 111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 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 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 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: 0.9980 chunk 37 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.4092 r_free = 0.4092 target = 0.176487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.122125 restraints weight = 7468.313| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.87 r_work: 0.3031 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6339 Z= 0.309 Angle : 0.545 6.049 8841 Z= 0.282 Chirality : 0.040 0.142 1015 Planarity : 0.004 0.063 953 Dihedral : 16.099 172.532 1417 Min Nonbonded Distance : 1.030 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.62 % Allowed : 11.93 % Favored : 84.45 % 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: -2.20 (0.31), residues: 638 helix: -1.07 (0.45), residues: 142 sheet: -2.71 (0.54), residues: 68 loop : -1.42 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 385 HIS 0.004 0.001 HIS B 257 PHE 0.019 0.002 PHE A 19 TYR 0.010 0.001 TYR B 447 ARG 0.003 0.000 ARG B 52 *********************** 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: 20 poor density : 92 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 33 SER cc_start: 0.8246 (t) cc_final: 0.7961 (t) REVERT: A 95 LYS cc_start: 0.7751 (mmtt) cc_final: 0.7410 (mmtp) REVERT: A 98 GLN cc_start: 0.8517 (mp-120) cc_final: 0.8189 (mm-40) REVERT: A 114 ASN cc_start: 0.8763 (m-40) cc_final: 0.8387 (m110) REVERT: B 58 MET cc_start: 0.9104 (mtp) cc_final: 0.8710 (mtp) REVERT: B 61 LYS cc_start: 0.9108 (mtpt) cc_final: 0.8726 (mtpp) REVERT: B 169 MET cc_start: 0.8871 (ttp) cc_final: 0.8543 (ptm) REVERT: B 185 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8518 (mt) REVERT: B 330 HIS cc_start: 0.7565 (m-70) cc_final: 0.6622 (m170) REVERT: B 334 ASN cc_start: 0.8412 (t0) cc_final: 0.8162 (p0) REVERT: B 391 ARG cc_start: 0.8290 (ttm170) cc_final: 0.7811 (mtp180) REVERT: B 395 ASN cc_start: 0.8518 (p0) cc_final: 0.8079 (p0) REVERT: B 444 PHE cc_start: 0.7886 (t80) cc_final: 0.7566 (t80) REVERT: B 499 ASN cc_start: 0.7666 (m110) cc_final: 0.7428 (m110) outliers start: 20 outliers final: 17 residues processed: 103 average time/residue: 0.1845 time to fit residues: 25.3156 Evaluate side-chains 107 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 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 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 153 MET Chi-restraints excluded: chain B residue 167 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 382 CYS Chi-restraints excluded: chain B residue 493 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 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 = 0.4080 r_free = 0.4080 target = 0.177151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118046 restraints weight = 7267.339| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.65 r_work: 0.3059 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6339 Z= 0.214 Angle : 0.499 5.261 8841 Z= 0.257 Chirality : 0.039 0.152 1015 Planarity : 0.004 0.077 953 Dihedral : 16.025 172.723 1417 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.62 % Allowed : 13.38 % 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: -1.93 (0.32), residues: 638 helix: -0.87 (0.45), residues: 143 sheet: -2.25 (0.59), residues: 60 loop : -1.33 (0.29), residues: 435 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 0.014 0.001 PHE A 19 TYR 0.008 0.001 TYR B 420 ARG 0.003 0.000 ARG A 78 *********************** 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 115 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 SER cc_start: 0.8100 (t) cc_final: 0.7847 (t) REVERT: A 95 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7321 (mmtp) REVERT: A 114 ASN cc_start: 0.8734 (m-40) cc_final: 0.8314 (m110) REVERT: B 58 MET cc_start: 0.9038 (mtp) cc_final: 0.8626 (mtp) REVERT: B 61 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8656 (mtpp) REVERT: B 169 MET cc_start: 0.8776 (ttp) cc_final: 0.8468 (ptm) REVERT: B 185 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8456 (mt) REVERT: B 330 HIS cc_start: 0.7540 (m-70) cc_final: 0.6532 (m-70) REVERT: B 391 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7775 (mtp180) REVERT: B 395 ASN cc_start: 0.8558 (p0) cc_final: 0.8128 (p0) REVERT: B 398 VAL cc_start: 0.9020 (t) cc_final: 0.8664 (p) REVERT: B 444 PHE cc_start: 0.7711 (t80) cc_final: 0.7410 (t80) REVERT: B 499 ASN cc_start: 0.7709 (m110) cc_final: 0.7473 (m-40) outliers start: 20 outliers final: 17 residues processed: 106 average time/residue: 0.1921 time to fit residues: 27.3422 Evaluate side-chains 111 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 97 THR Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 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 382 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.7222 > 50: distance: 16 - 22: 19.998 distance: 22 - 23: 50.547 distance: 23 - 24: 22.593 distance: 23 - 26: 43.600 distance: 24 - 25: 19.790 distance: 24 - 29: 19.611 distance: 26 - 27: 37.148 distance: 26 - 28: 18.416 distance: 29 - 30: 59.408 distance: 30 - 31: 27.715 distance: 31 - 32: 5.473 distance: 33 - 34: 19.854 distance: 34 - 35: 16.407 distance: 35 - 36: 18.655 distance: 37 - 38: 11.478 distance: 38 - 39: 8.551 distance: 38 - 40: 7.265 distance: 41 - 42: 10.453 distance: 42 - 43: 25.193 distance: 42 - 45: 9.856 distance: 43 - 44: 35.072 distance: 43 - 49: 21.264 distance: 44 - 72: 57.442 distance: 45 - 46: 3.359 distance: 46 - 47: 14.087 distance: 46 - 48: 29.429 distance: 49 - 50: 24.725 distance: 50 - 51: 20.194 distance: 50 - 53: 10.604 distance: 51 - 52: 24.991 distance: 51 - 58: 20.151 distance: 53 - 54: 27.395 distance: 54 - 55: 27.301 distance: 55 - 56: 20.654 distance: 55 - 57: 33.538 distance: 58 - 59: 22.441 distance: 59 - 60: 27.405 distance: 60 - 61: 23.184 distance: 60 - 64: 27.725 distance: 64 - 65: 28.347 distance: 65 - 66: 59.954 distance: 65 - 68: 25.619 distance: 66 - 67: 42.990 distance: 66 - 72: 40.803 distance: 68 - 69: 17.810 distance: 69 - 70: 36.951 distance: 69 - 71: 3.016 distance: 72 - 73: 42.187 distance: 73 - 74: 61.361 distance: 74 - 75: 45.706 distance: 74 - 82: 41.146 distance: 76 - 77: 15.886 distance: 77 - 78: 6.051 distance: 77 - 79: 41.537 distance: 78 - 80: 35.436 distance: 79 - 81: 8.133 distance: 80 - 81: 48.856 distance: 81 - 169: 36.113 distance: 82 - 83: 17.152 distance: 83 - 84: 27.612 distance: 83 - 86: 45.850 distance: 84 - 85: 45.324 distance: 84 - 90: 21.221 distance: 86 - 87: 25.126 distance: 87 - 88: 24.898 distance: 87 - 89: 18.299 distance: 91 - 92: 15.094 distance: 91 - 94: 19.831 distance: 92 - 93: 4.468 distance: 92 - 98: 22.688 distance: 94 - 95: 23.660 distance: 95 - 96: 23.073 distance: 95 - 97: 31.030