Starting phenix.real_space_refine on Mon Mar 11 08:54:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/03_2024/7upi_26667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/03_2024/7upi_26667.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/03_2024/7upi_26667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/03_2024/7upi_26667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/03_2024/7upi_26667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7upi_26667/03_2024/7upi_26667_updated.pdb" } resolution = 2.89 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= 0.000 sd= 0.001 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: 8 Type Number sf(0) Gaussians Mn 2 7.51 5 P 3 5.49 5 Mg 1 5.21 5 S 40 5.16 5 Cl 1 4.86 5 C 4937 2.51 5 N 1324 2.21 5 O 1467 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7775 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1406 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 165} Chain: "B" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2356 Classifications: {'peptide': 293} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 279} Chain: "C" Number of atoms: 3977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3977 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 27, 'TRANS': 477} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CL': 1, ' MN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.59, per 1000 atoms: 0.59 Number of scatterers: 7775 At special positions: 0 Unit cell: (101.46, 92.916, 92.916, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Mn 2 24.99 Cl 1 17.00 S 40 16.00 P 3 15.00 Mg 1 11.99 O 1467 8.00 N 1324 7.00 C 4937 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 - 3.50 Amino acid : False - 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: 2.94 Conformation dependent library (CDL) restraints added in 1.5 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 6 sheets defined 28.7% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'A' and resid 97 through 114 removed outlier: 3.536A pdb=" N VAL A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASP A 104 " --> pdb=" O PHE A 100 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.950A pdb=" N PHE A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 17 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 69 through 79 Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 128 through 134 removed outlier: 3.572A pdb=" N ILE B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 143 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.868A pdb=" N CYS B 158 " --> pdb=" O ASP B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 229 through 239 Processing helix chain 'B' and resid 272 through 274 No H-bonds generated for 'chain 'B' and resid 272 through 274' Processing helix chain 'C' and resid 88 through 100 Processing helix chain 'C' and resid 117 through 121 Processing helix chain 'C' and resid 140 through 144 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 186 through 190 removed outlier: 3.658A pdb=" N ARG C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 186 through 190' Processing helix chain 'C' and resid 209 through 213 removed outlier: 3.560A pdb=" N LYS C 212 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.534A pdb=" N GLY C 235 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.968A pdb=" N GLY C 281 " --> pdb=" O ASP C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 326 through 329 No H-bonds generated for 'chain 'C' and resid 326 through 329' Processing helix chain 'C' and resid 351 through 354 Processing helix chain 'C' and resid 396 through 400 removed outlier: 4.599A pdb=" N GLY C 399 " --> pdb=" O LEU C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 419 through 423 removed outlier: 3.584A pdb=" N SER C 422 " --> pdb=" O GLU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 465 through 469 Processing helix chain 'C' and resid 488 through 492 removed outlier: 3.833A pdb=" N GLY C 491 " --> pdb=" O ARG C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.585A pdb=" N GLY C 514 " --> pdb=" O GLU C 511 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 558 through 563 Processing helix chain 'C' and resid 565 through 575 Processing sheet with id= A, first strand: chain 'A' and resid 151 through 154 removed outlier: 6.820A pdb=" N PHE A 88 " --> pdb=" O ILE A 122 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL A 124 " --> pdb=" O PHE A 88 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE A 90 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ASN A 126 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TYR A 92 " --> pdb=" O ASN A 126 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 52 through 55 removed outlier: 6.889A pdb=" N ALA B 162 " --> pdb=" O LEU B 53 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LEU B 55 " --> pdb=" O ALA B 162 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE B 164 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 243 " --> pdb=" O PHE B 170 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N CYS B 172 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N CYS B 245 " --> pdb=" O CYS B 172 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 118 through 120 removed outlier: 6.221A pdb=" N TYR B 87 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LYS B 60 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 216 through 218 Processing sheet with id= E, first strand: chain 'C' and resid 65 through 68 Processing sheet with id= F, first strand: chain 'C' and resid 104 through 106 removed outlier: 6.430A pdb=" N GLU C 127 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N THR C 150 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N MET C 173 " --> pdb=" O LEU C 151 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR C 196 " --> pdb=" O LEU C 174 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET C 219 " --> pdb=" O LEU C 197 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N THR C 242 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASN C 265 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ARG C 288 " --> pdb=" O LEU C 266 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU C 311 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N SER C 335 " --> pdb=" O LEU C 312 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N SER C 359 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LYS C 383 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N GLU C 406 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 429 " --> pdb=" O LEU C 407 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLU C 452 " --> pdb=" O LEU C 430 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS C 475 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N HIS C 498 " --> pdb=" O LEU C 476 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLU C 521 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE C 545 " --> pdb=" O LEU C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 185 hydrogen bonds defined for protein. 462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1680 1.33 - 1.45: 1573 1.45 - 1.57: 4598 1.57 - 1.69: 5 1.69 - 1.81: 59 Bond restraints: 7915 Sorted by residual: bond pdb=" N VAL A 39 " pdb=" CA VAL A 39 " ideal model delta sigma weight residual 1.460 1.487 -0.027 7.30e-03 1.88e+04 1.37e+01 bond pdb=" N GLN B 249 " pdb=" CA GLN B 249 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.21e-02 6.83e+03 6.90e+00 bond pdb=" N HIS B 248 " pdb=" CA HIS B 248 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.12e+00 bond pdb=" C LYS A 127 " pdb=" N VAL A 128 " ideal model delta sigma weight residual 1.336 1.365 -0.028 1.17e-02 7.31e+03 5.82e+00 bond pdb=" C2 GTP A 201 " pdb=" N3 GTP A 201 " ideal model delta sigma weight residual 1.380 1.332 0.048 2.00e-02 2.50e+03 5.67e+00 ... (remaining 7910 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.56: 251 106.56 - 113.41: 4398 113.41 - 120.26: 2739 120.26 - 127.11: 3255 127.11 - 133.96: 81 Bond angle restraints: 10724 Sorted by residual: angle pdb=" PB GTP A 201 " pdb=" O3B GTP A 201 " pdb=" PG GTP A 201 " ideal model delta sigma weight residual 120.50 132.61 -12.11 3.00e+00 1.11e-01 1.63e+01 angle pdb=" PA GTP A 201 " pdb=" O3A GTP A 201 " pdb=" PB GTP A 201 " ideal model delta sigma weight residual 120.50 131.86 -11.36 3.00e+00 1.11e-01 1.43e+01 angle pdb=" C1' GTP A 201 " pdb=" C2' GTP A 201 " pdb=" C3' GTP A 201 " ideal model delta sigma weight residual 111.00 99.71 11.29 3.00e+00 1.11e-01 1.42e+01 angle pdb=" CA GLN B 68 " pdb=" C GLN B 68 " pdb=" O GLN B 68 " ideal model delta sigma weight residual 122.41 118.10 4.31 1.21e+00 6.83e-01 1.27e+01 angle pdb=" C TYR B 70 " pdb=" CA TYR B 70 " pdb=" CB TYR B 70 " ideal model delta sigma weight residual 110.67 117.48 -6.81 1.92e+00 2.71e-01 1.26e+01 ... (remaining 10719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.99: 4829 28.99 - 57.98: 25 57.98 - 86.97: 1 86.97 - 115.97: 2 115.97 - 144.96: 4 Dihedral angle restraints: 4861 sinusoidal: 2022 harmonic: 2839 Sorted by residual: dihedral pdb=" C8 GTP A 201 " pdb=" C1' GTP A 201 " pdb=" N9 GTP A 201 " pdb=" O4' GTP A 201 " ideal model delta sinusoidal sigma weight residual 104.59 -40.36 144.96 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O3B GTP A 201 " pdb=" O3A GTP A 201 " pdb=" PB GTP A 201 " pdb=" PA GTP A 201 " ideal model delta sinusoidal sigma weight residual -68.92 74.77 -143.69 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' GTP A 201 " pdb=" O5' GTP A 201 " pdb=" PA GTP A 201 " pdb=" O3A GTP A 201 " ideal model delta sinusoidal sigma weight residual 69.27 -60.23 129.50 1 2.00e+01 2.50e-03 3.93e+01 ... (remaining 4858 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1110 0.059 - 0.118: 117 0.118 - 0.177: 8 0.177 - 0.236: 3 0.236 - 0.296: 1 Chirality restraints: 1239 Sorted by residual: chirality pdb=" C3' GTP A 201 " pdb=" C2' GTP A 201 " pdb=" C4' GTP A 201 " pdb=" O3' GTP A 201 " both_signs ideal model delta sigma weight residual False -2.47 -2.77 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB VAL A 128 " pdb=" CA VAL A 128 " pdb=" CG1 VAL A 128 " pdb=" CG2 VAL A 128 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL A 128 " pdb=" N VAL A 128 " pdb=" C VAL A 128 " pdb=" CB VAL A 128 " both_signs ideal model delta sigma weight residual False 2.44 2.25 0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 1236 not shown) Planarity restraints: 1376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 70 " -0.029 2.00e-02 2.50e+03 1.69e-02 5.71e+00 pdb=" CG TYR B 70 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 70 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 70 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 70 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 70 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 70 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 70 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 67 " 0.005 2.00e-02 2.50e+03 1.11e-02 1.24e+00 pdb=" C GLY B 67 " -0.019 2.00e-02 2.50e+03 pdb=" O GLY B 67 " 0.007 2.00e-02 2.50e+03 pdb=" N GLN B 68 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 70 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.21e+00 pdb=" C TYR B 70 " 0.019 2.00e-02 2.50e+03 pdb=" O TYR B 70 " -0.007 2.00e-02 2.50e+03 pdb=" N ASP B 71 " -0.007 2.00e-02 2.50e+03 ... (remaining 1373 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 16 2.45 - 3.07: 5141 3.07 - 3.68: 11318 3.68 - 4.29: 18468 4.29 - 4.90: 30428 Nonbonded interactions: 65371 Sorted by model distance: nonbonded pdb=" OD1 ASN B 124 " pdb="MN MN B 401 " model vdw 1.843 2.320 nonbonded pdb=" OD2 ASP B 92 " pdb="MN MN B 401 " model vdw 1.934 2.320 nonbonded pdb=" OG SER A 27 " pdb="MG MG A 202 " model vdw 1.984 2.170 nonbonded pdb=" O2G GTP A 201 " pdb="MG MG A 202 " model vdw 1.984 2.170 nonbonded pdb=" NE2 HIS B 66 " pdb="MN MN B 402 " model vdw 2.052 2.400 ... (remaining 65366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.090 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: 4.120 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.490 Find NCS groups from input model: 0.210 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:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 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 : 0.002 0.071 7915 Z= 0.170 Angle : 0.547 12.107 10724 Z= 0.271 Chirality : 0.041 0.296 1239 Planarity : 0.003 0.027 1376 Dihedral : 9.087 144.958 3017 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.12 (0.28), residues: 964 helix: -0.18 (0.30), residues: 326 sheet: -0.36 (0.39), residues: 196 loop : 0.38 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 149 HIS 0.003 0.000 HIS B 248 PHE 0.005 0.001 PHE B 118 TYR 0.036 0.001 TYR B 70 ARG 0.001 0.000 ARG C 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7958 (mp0) cc_final: 0.7721 (mp0) REVERT: C 567 PHE cc_start: 0.8644 (m-80) cc_final: 0.8328 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.4930 time to fit residues: 105.8061 Evaluate side-chains 42 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.0870 chunk 49 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7915 Z= 0.209 Angle : 0.468 8.578 10724 Z= 0.235 Chirality : 0.040 0.131 1239 Planarity : 0.003 0.056 1376 Dihedral : 9.754 147.626 1055 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.79 % Allowed : 4.98 % Favored : 94.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.05 (0.28), residues: 964 helix: -0.04 (0.31), residues: 326 sheet: -0.50 (0.38), residues: 196 loop : 0.45 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 401 HIS 0.002 0.001 HIS B 239 PHE 0.014 0.001 PHE C 535 TYR 0.012 0.001 TYR B 70 ARG 0.008 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: C 567 PHE cc_start: 0.8656 (m-80) cc_final: 0.8297 (m-80) outliers start: 7 outliers final: 1 residues processed: 47 average time/residue: 1.2421 time to fit residues: 62.7458 Evaluate side-chains 40 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 0.0000 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7915 Z= 0.231 Angle : 0.473 8.388 10724 Z= 0.236 Chirality : 0.040 0.128 1239 Planarity : 0.003 0.031 1376 Dihedral : 9.324 146.407 1055 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.57 % Allowed : 5.77 % Favored : 93.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.11 (0.28), residues: 964 helix: -0.08 (0.31), residues: 325 sheet: -0.66 (0.38), residues: 191 loop : 0.45 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 401 HIS 0.002 0.001 HIS B 66 PHE 0.007 0.001 PHE C 398 TYR 0.015 0.001 TYR B 70 ARG 0.006 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 41 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8002 (mp0) cc_final: 0.7647 (mp0) REVERT: C 94 LEU cc_start: 0.9466 (mt) cc_final: 0.9230 (mp) REVERT: C 567 PHE cc_start: 0.8704 (m-80) cc_final: 0.8341 (m-80) outliers start: 5 outliers final: 1 residues processed: 45 average time/residue: 1.2931 time to fit residues: 62.5866 Evaluate side-chains 38 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 0.3980 chunk 92 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7915 Z= 0.204 Angle : 0.471 10.863 10724 Z= 0.233 Chirality : 0.039 0.128 1239 Planarity : 0.003 0.034 1376 Dihedral : 9.070 146.478 1055 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.68 % Allowed : 5.54 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.12 (0.28), residues: 964 helix: -0.11 (0.31), residues: 326 sheet: -0.69 (0.38), residues: 191 loop : 0.49 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 149 HIS 0.002 0.001 HIS B 239 PHE 0.007 0.001 PHE C 398 TYR 0.014 0.001 TYR B 70 ARG 0.003 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: C 94 LEU cc_start: 0.9466 (mt) cc_final: 0.9203 (mp) REVERT: C 567 PHE cc_start: 0.8674 (m-80) cc_final: 0.8371 (m-80) outliers start: 6 outliers final: 1 residues processed: 43 average time/residue: 1.3537 time to fit residues: 62.4354 Evaluate side-chains 40 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 7915 Z= 0.315 Angle : 0.525 12.311 10724 Z= 0.259 Chirality : 0.040 0.128 1239 Planarity : 0.003 0.035 1376 Dihedral : 8.945 148.490 1055 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.79 % Allowed : 5.77 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.22 (0.28), residues: 964 helix: -0.19 (0.31), residues: 328 sheet: -0.76 (0.38), residues: 191 loop : 0.45 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 401 HIS 0.004 0.001 HIS B 239 PHE 0.007 0.001 PHE A 106 TYR 0.015 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 567 PHE cc_start: 0.8716 (m-80) cc_final: 0.8366 (m-80) outliers start: 7 outliers final: 1 residues processed: 45 average time/residue: 1.1845 time to fit residues: 57.5943 Evaluate side-chains 38 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7915 Z= 0.152 Angle : 0.487 12.657 10724 Z= 0.238 Chirality : 0.039 0.128 1239 Planarity : 0.003 0.038 1376 Dihedral : 8.490 146.669 1055 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.68 % Allowed : 6.22 % Favored : 93.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.18 (0.28), residues: 964 helix: -0.16 (0.31), residues: 326 sheet: -0.74 (0.39), residues: 187 loop : 0.45 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 401 HIS 0.003 0.001 HIS B 239 PHE 0.007 0.001 PHE C 398 TYR 0.012 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7993 (mp0) cc_final: 0.7783 (mp0) REVERT: C 465 ASN cc_start: 0.9296 (OUTLIER) cc_final: 0.9003 (m110) REVERT: C 567 PHE cc_start: 0.8725 (m-80) cc_final: 0.8390 (m-80) outliers start: 6 outliers final: 0 residues processed: 42 average time/residue: 1.3064 time to fit residues: 58.7218 Evaluate side-chains 38 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 465 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 51 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 575 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8810 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7915 Z= 0.198 Angle : 0.512 12.640 10724 Z= 0.247 Chirality : 0.039 0.129 1239 Planarity : 0.003 0.035 1376 Dihedral : 8.293 145.173 1055 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.34 % Allowed : 6.79 % Favored : 92.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.25 (0.28), residues: 964 helix: -0.26 (0.31), residues: 328 sheet: -0.75 (0.39), residues: 187 loop : 0.43 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 206 HIS 0.003 0.001 HIS B 239 PHE 0.014 0.001 PHE C 535 TYR 0.012 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 567 PHE cc_start: 0.8734 (m-80) cc_final: 0.8396 (m-80) outliers start: 3 outliers final: 1 residues processed: 39 average time/residue: 1.3084 time to fit residues: 54.7543 Evaluate side-chains 38 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.1980 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7915 Z= 0.189 Angle : 0.514 11.653 10724 Z= 0.248 Chirality : 0.040 0.170 1239 Planarity : 0.003 0.034 1376 Dihedral : 8.106 143.307 1055 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.45 % Allowed : 7.01 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % 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: -0.23 (0.28), residues: 964 helix: -0.27 (0.31), residues: 326 sheet: -0.73 (0.39), residues: 187 loop : 0.46 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 206 HIS 0.004 0.001 HIS B 239 PHE 0.009 0.001 PHE C 398 TYR 0.012 0.001 TYR B 70 ARG 0.002 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 465 ASN cc_start: 0.9304 (OUTLIER) cc_final: 0.9024 (m110) REVERT: C 567 PHE cc_start: 0.8732 (m-80) cc_final: 0.8392 (m-80) outliers start: 4 outliers final: 1 residues processed: 40 average time/residue: 1.3861 time to fit residues: 59.3677 Evaluate side-chains 39 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 465 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6657 > 50: distance: 54 - 58: 7.878 distance: 58 - 59: 19.235 distance: 59 - 60: 22.073 distance: 59 - 62: 11.394 distance: 60 - 61: 8.789 distance: 60 - 64: 13.006 distance: 62 - 63: 16.109 distance: 64 - 65: 11.484 distance: 65 - 66: 40.545 distance: 65 - 68: 43.091 distance: 66 - 67: 10.268 distance: 66 - 72: 16.775 distance: 68 - 69: 20.430 distance: 69 - 70: 23.880 distance: 69 - 71: 24.924 distance: 72 - 73: 28.800 distance: 72 - 78: 28.248 distance: 73 - 74: 11.753 distance: 74 - 75: 11.097 distance: 74 - 79: 29.256 distance: 76 - 77: 15.912 distance: 77 - 78: 32.847 distance: 79 - 80: 32.591 distance: 80 - 81: 16.744 distance: 80 - 83: 5.572 distance: 81 - 82: 19.502 distance: 81 - 87: 9.774 distance: 82 - 104: 10.361 distance: 83 - 84: 15.619 distance: 84 - 85: 9.010 distance: 84 - 86: 33.753 distance: 87 - 88: 17.789 distance: 88 - 89: 46.057 distance: 88 - 91: 12.555 distance: 89 - 90: 25.261 distance: 89 - 96: 35.374 distance: 90 - 109: 33.290 distance: 91 - 92: 37.688 distance: 92 - 93: 9.188 distance: 93 - 94: 34.234 distance: 93 - 95: 26.170 distance: 96 - 97: 9.130 distance: 97 - 98: 6.340 distance: 97 - 100: 4.048 distance: 98 - 99: 38.582 distance: 98 - 104: 17.181 distance: 100 - 101: 36.193 distance: 100 - 102: 6.225 distance: 101 - 103: 32.013 distance: 104 - 105: 15.976 distance: 105 - 106: 23.539 distance: 105 - 108: 13.947 distance: 106 - 107: 36.537 distance: 106 - 109: 17.442 distance: 109 - 110: 15.048 distance: 110 - 111: 10.471 distance: 110 - 113: 19.546 distance: 111 - 112: 4.918 distance: 111 - 121: 24.128 distance: 113 - 114: 27.037 distance: 114 - 115: 13.692 distance: 114 - 116: 36.463 distance: 115 - 117: 13.101 distance: 117 - 119: 30.784 distance: 118 - 119: 18.793 distance: 119 - 120: 30.779 distance: 121 - 122: 32.005 distance: 122 - 123: 16.452 distance: 122 - 125: 12.566 distance: 123 - 124: 12.763 distance: 123 - 129: 28.303 distance: 125 - 126: 27.173 distance: 126 - 127: 20.333 distance: 126 - 128: 40.625 distance: 129 - 130: 25.105 distance: 130 - 131: 15.382 distance: 130 - 133: 10.228 distance: 131 - 132: 16.376 distance: 131 - 138: 21.692 distance: 133 - 134: 23.113 distance: 134 - 135: 8.611 distance: 135 - 136: 15.336 distance: 136 - 137: 7.594