Starting phenix.real_space_refine on Tue Feb 13 11:53:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z52_14513/02_2024/7z52_14513_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z52_14513/02_2024/7z52_14513.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z52_14513/02_2024/7z52_14513.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z52_14513/02_2024/7z52_14513.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z52_14513/02_2024/7z52_14513_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z52_14513/02_2024/7z52_14513_updated.pdb" } 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= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 45 5.16 5 C 3731 2.51 5 N 1002 2.21 5 O 1126 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 121": "OD1" <-> "OD2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "B PHE 480": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 955": "OE1" <-> "OE2" Residue "B GLU 1018": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5911 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 706, 5494 Classifications: {'peptide': 706} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 680} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 100 Classifications: {'RNA': 5} Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 3} Chain: "A" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 290 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 3, 'TRANS': 36} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 3.75, per 1000 atoms: 0.63 Number of scatterers: 5911 At special positions: 0 Unit cell: (87.6736, 88.5248, 77.4592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 7 15.00 O 1126 8.00 N 1002 7.00 C 3731 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: 2.05 Conformation dependent library (CDL) restraints added in 1.3 seconds 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 3 sheets defined 43.6% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 168 through 180 Processing helix chain 'B' and resid 192 through 203 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 254 through 256 No H-bonds generated for 'chain 'B' and resid 254 through 256' Processing helix chain 'B' and resid 264 through 272 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.516A pdb=" N ALA B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 352 Processing helix chain 'B' and resid 373 through 383 removed outlier: 3.504A pdb=" N ILE B 377 " --> pdb=" O ASN B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.574A pdb=" N GLU B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 437 removed outlier: 3.889A pdb=" N ASN B 426 " --> pdb=" O GLU B 422 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER B 432 " --> pdb=" O ILE B 428 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP B 433 " --> pdb=" O ASP B 429 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N GLU B 434 " --> pdb=" O CYS B 430 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ASP B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS B 437 " --> pdb=" O ASP B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 Proline residue: B 446 - end of helix Processing helix chain 'B' and resid 461 through 473 removed outlier: 3.636A pdb=" N GLU B 465 " --> pdb=" O PRO B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 485 No H-bonds generated for 'chain 'B' and resid 483 through 485' Processing helix chain 'B' and resid 514 through 523 removed outlier: 4.150A pdb=" N ARG B 523 " --> pdb=" O GLN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 575 Processing helix chain 'B' and resid 581 through 586 Processing helix chain 'B' and resid 589 through 595 Processing helix chain 'B' and resid 832 through 842 Processing helix chain 'B' and resid 849 through 861 Processing helix chain 'B' and resid 872 through 879 removed outlier: 3.617A pdb=" N VAL B 876 " --> pdb=" O MET B 872 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA B 877 " --> pdb=" O LYS B 873 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU B 879 " --> pdb=" O ARG B 875 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 894 Processing helix chain 'B' and resid 903 through 906 No H-bonds generated for 'chain 'B' and resid 903 through 906' Processing helix chain 'B' and resid 908 through 912 Processing helix chain 'B' and resid 926 through 947 Proline residue: B 931 - end of helix removed outlier: 3.528A pdb=" N VAL B 945 " --> pdb=" O ARG B 941 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 961 Processing helix chain 'B' and resid 967 through 975 removed outlier: 3.790A pdb=" N THR B 975 " --> pdb=" O TYR B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 982 No H-bonds generated for 'chain 'B' and resid 979 through 982' Processing helix chain 'B' and resid 990 through 1011 removed outlier: 3.540A pdb=" N GLN B1009 " --> pdb=" O ARG B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1028 removed outlier: 3.527A pdb=" N ALA B1024 " --> pdb=" O GLU B1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 684 through 691 removed outlier: 3.674A pdb=" N LEU A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 99 through 101 removed outlier: 7.261A pdb=" N SER B 156 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE B 307 " --> pdb=" O SER B 156 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU B 158 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ARG B 184 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 249 " --> pdb=" O ARG B 184 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 186 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N PHE B 251 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N THR B 188 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N GLY B 210 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR B 228 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N MET B 212 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 452 through 455 removed outlier: 6.595A pdb=" N ALA B 478 " --> pdb=" O GLY B 453 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N HIS B 455 " --> pdb=" O ALA B 478 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE B 480 " --> pdb=" O HIS B 455 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 389 " --> pdb=" O LEU B 479 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N ALA B 481 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE B 391 " --> pdb=" O ALA B 481 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR B 495 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N PHE B 392 " --> pdb=" O THR B 495 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 497 " --> pdb=" O PHE B 392 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N VAL B 496 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 534 " --> pdb=" O VAL B 496 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N PHE B 498 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 536 " --> pdb=" O PHE B 498 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N VAL B 535 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN B 317 " --> pdb=" O VAL B 535 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU B 537 " --> pdb=" O GLN B 317 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR B 319 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL B 539 " --> pdb=" O TYR B 319 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE B 321 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL B 332 " --> pdb=" O HIS B 318 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE B 320 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU B 330 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 502 through 504 193 hydrogen bonds defined for protein. 564 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: 1.92 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1865 1.34 - 1.45: 784 1.45 - 1.57: 3293 1.57 - 1.69: 13 1.69 - 1.81: 75 Bond restraints: 6030 Sorted by residual: bond pdb=" O3A ANP B2001 " pdb=" PB ANP B2001 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.09e+01 bond pdb=" O5' ANP B2001 " pdb=" PA ANP B2001 " ideal model delta sigma weight residual 1.655 1.580 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 1.457 1.496 -0.039 1.29e-02 6.01e+03 9.03e+00 bond pdb=" N GLN B 387 " pdb=" CA GLN B 387 " ideal model delta sigma weight residual 1.453 1.492 -0.039 1.44e-02 4.82e+03 7.41e+00 bond pdb=" O2B ANP B2001 " pdb=" PB ANP B2001 " ideal model delta sigma weight residual 1.508 1.556 -0.048 2.00e-02 2.50e+03 5.87e+00 ... (remaining 6025 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.21: 134 105.21 - 112.40: 3059 112.40 - 119.58: 2056 119.58 - 126.77: 2858 126.77 - 133.96: 70 Bond angle restraints: 8177 Sorted by residual: angle pdb=" N VAL B 601 " pdb=" CA VAL B 601 " pdb=" C VAL B 601 " ideal model delta sigma weight residual 112.96 107.96 5.00 1.00e+00 1.00e+00 2.50e+01 angle pdb=" C HIS B 300 " pdb=" N LYS B 301 " pdb=" CA LYS B 301 " ideal model delta sigma weight residual 121.54 129.25 -7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" O1B ANP B2001 " pdb=" PB ANP B2001 " pdb=" O2B ANP B2001 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" N PRO B 97 " pdb=" CD PRO B 97 " pdb=" CG PRO B 97 " ideal model delta sigma weight residual 103.20 98.02 5.18 1.50e+00 4.44e-01 1.19e+01 angle pdb=" CA PRO B 97 " pdb=" N PRO B 97 " pdb=" CD PRO B 97 " ideal model delta sigma weight residual 112.00 107.53 4.47 1.40e+00 5.10e-01 1.02e+01 ... (remaining 8172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.88: 3609 34.88 - 69.75: 79 69.75 - 104.63: 8 104.63 - 139.50: 1 139.50 - 174.38: 1 Dihedral angle restraints: 3698 sinusoidal: 1518 harmonic: 2180 Sorted by residual: dihedral pdb=" O4' U R 1 " pdb=" C1' U R 1 " pdb=" N1 U R 1 " pdb=" C2 U R 1 " ideal model delta sinusoidal sigma weight residual -128.00 46.38 -174.38 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' U R 2 " pdb=" C1' U R 2 " pdb=" N1 U R 2 " pdb=" C2 U R 2 " ideal model delta sinusoidal sigma weight residual -160.00 -54.47 -105.53 1 1.50e+01 4.44e-03 5.41e+01 dihedral pdb=" CA GLN B1009 " pdb=" C GLN B1009 " pdb=" N ALA B1010 " pdb=" CA ALA B1010 " ideal model delta harmonic sigma weight residual 180.00 152.68 27.32 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 3695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 759 0.054 - 0.107: 156 0.107 - 0.161: 22 0.161 - 0.215: 0 0.215 - 0.268: 1 Chirality restraints: 938 Sorted by residual: chirality pdb=" C3' ANP B2001 " pdb=" C2' ANP B2001 " pdb=" C4' ANP B2001 " pdb=" O3' ANP B2001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA VAL B 185 " pdb=" N VAL B 185 " pdb=" C VAL B 185 " pdb=" CB VAL B 185 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA ILE B 139 " pdb=" N ILE B 139 " pdb=" C ILE B 139 " pdb=" CB ILE B 139 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 935 not shown) Planarity restraints: 1033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 921 " 0.032 5.00e-02 4.00e+02 4.86e-02 3.77e+00 pdb=" N PRO B 922 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 922 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 922 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 560 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.76e+00 pdb=" C ASN B 560 " 0.029 2.00e-02 2.50e+03 pdb=" O ASN B 560 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 561 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 598 " -0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO B 599 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 599 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 599 " -0.022 5.00e-02 4.00e+02 ... (remaining 1030 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 621 2.75 - 3.29: 5760 3.29 - 3.82: 9247 3.82 - 4.36: 11268 4.36 - 4.90: 19334 Nonbonded interactions: 46230 Sorted by model distance: nonbonded pdb=" O LEU B 404 " pdb=" OG1 THR B 407 " model vdw 2.209 2.440 nonbonded pdb=" O THR B 972 " pdb=" OG1 THR B 975 " model vdw 2.269 2.440 nonbonded pdb=" NE2 GLN B 144 " pdb=" O GLY B 166 " model vdw 2.282 2.520 nonbonded pdb=" OD1 ASN B 572 " pdb=" NH2 ARG B 575 " model vdw 2.290 2.520 nonbonded pdb=" NZ LYS B 167 " pdb=" O SER B 283 " model vdw 2.291 2.520 ... (remaining 46225 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.720 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.610 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 0.004 0.143 6030 Z= 0.282 Angle : 0.660 10.868 8177 Z= 0.348 Chirality : 0.043 0.268 938 Planarity : 0.004 0.049 1033 Dihedral : 15.636 174.376 2280 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.27 % Allowed : 1.76 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.69 (0.30), residues: 738 helix: -0.40 (0.28), residues: 362 sheet: 0.44 (0.60), residues: 82 loop : -2.51 (0.30), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 266 HIS 0.003 0.001 HIS B 456 PHE 0.015 0.002 PHE B 563 TYR 0.011 0.001 TYR B 590 ARG 0.005 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 203 TYR cc_start: 0.8664 (t80) cc_final: 0.8450 (t80) REVERT: B 244 ARG cc_start: 0.6399 (ttm-80) cc_final: 0.6030 (tpp-160) REVERT: B 256 TYR cc_start: 0.6257 (m-80) cc_final: 0.6005 (m-80) REVERT: B 569 MET cc_start: 0.8217 (ttm) cc_final: 0.7885 (ttm) REVERT: B 590 TYR cc_start: 0.8272 (t80) cc_final: 0.7560 (t80) REVERT: B 935 MET cc_start: 0.8169 (tmm) cc_final: 0.7894 (tmm) REVERT: B 987 ASP cc_start: 0.7078 (p0) cc_final: 0.6339 (p0) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2082 time to fit residues: 32.4702 Evaluate side-chains 71 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.0370 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 255 HIS B 291 GLN B 302 GLN ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6030 Z= 0.187 Angle : 0.538 9.622 8177 Z= 0.273 Chirality : 0.041 0.159 938 Planarity : 0.004 0.035 1033 Dihedral : 11.410 172.989 907 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.35 % Favored : 90.51 % Rotamer: Outliers : 1.80 % Allowed : 7.86 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -1.21 (0.30), residues: 738 helix: 0.33 (0.28), residues: 355 sheet: 0.56 (0.63), residues: 78 loop : -2.62 (0.30), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 295 HIS 0.003 0.001 HIS B 456 PHE 0.012 0.001 PHE B 504 TYR 0.008 0.001 TYR B 590 ARG 0.002 0.000 ARG B 875 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 569 MET cc_start: 0.8250 (ttm) cc_final: 0.7920 (ttm) REVERT: B 590 TYR cc_start: 0.8312 (t80) cc_final: 0.7538 (t80) REVERT: B 987 ASP cc_start: 0.7172 (p0) cc_final: 0.6489 (p0) REVERT: A 684 MET cc_start: 0.5237 (tpp) cc_final: 0.5012 (ttp) outliers start: 11 outliers final: 8 residues processed: 79 average time/residue: 0.1536 time to fit residues: 16.8187 Evaluate side-chains 74 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 559 LEU Chi-restraints excluded: chain A residue 663 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 0.0070 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6030 Z= 0.194 Angle : 0.518 9.397 8177 Z= 0.263 Chirality : 0.041 0.139 938 Planarity : 0.003 0.033 1033 Dihedral : 11.300 174.074 907 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.28 % Rotamer: Outliers : 1.80 % Allowed : 10.31 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.85 (0.31), residues: 738 helix: 0.52 (0.28), residues: 366 sheet: 0.68 (0.62), residues: 78 loop : -2.39 (0.31), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 266 HIS 0.004 0.001 HIS B 300 PHE 0.010 0.001 PHE B 424 TYR 0.007 0.001 TYR B 590 ARG 0.003 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 68 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 569 MET cc_start: 0.8266 (ttm) cc_final: 0.8009 (ttm) REVERT: B 590 TYR cc_start: 0.8363 (t80) cc_final: 0.7580 (t80) outliers start: 11 outliers final: 7 residues processed: 74 average time/residue: 0.1875 time to fit residues: 18.8556 Evaluate side-chains 72 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 65 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 105 GLU Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain A residue 663 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 64 optimal weight: 0.0020 chunk 19 optimal weight: 1.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6030 Z= 0.190 Angle : 0.497 9.894 8177 Z= 0.253 Chirality : 0.040 0.138 938 Planarity : 0.003 0.033 1033 Dihedral : 11.153 173.602 907 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.27 % Favored : 91.60 % Rotamer: Outliers : 2.29 % Allowed : 11.78 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.74 (0.31), residues: 738 helix: 0.75 (0.28), residues: 360 sheet: 0.66 (0.62), residues: 78 loop : -2.45 (0.32), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 266 HIS 0.004 0.001 HIS B 300 PHE 0.009 0.001 PHE B 281 TYR 0.019 0.001 TYR B 203 ARG 0.002 0.000 ARG B 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 73 time to evaluate : 0.629 Fit side-chains REVERT: B 569 MET cc_start: 0.8255 (ttm) cc_final: 0.8036 (ttm) REVERT: B 590 TYR cc_start: 0.8395 (t80) cc_final: 0.7616 (t80) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.1839 time to fit residues: 19.9775 Evaluate side-chains 73 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain A residue 663 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6030 Z= 0.279 Angle : 0.552 10.649 8177 Z= 0.283 Chirality : 0.042 0.139 938 Planarity : 0.003 0.033 1033 Dihedral : 11.334 172.473 907 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.13 % Favored : 91.73 % Rotamer: Outliers : 2.95 % Allowed : 13.26 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.78 (0.31), residues: 738 helix: 0.66 (0.28), residues: 357 sheet: 0.29 (0.60), residues: 83 loop : -2.29 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 266 HIS 0.007 0.001 HIS B 300 PHE 0.014 0.002 PHE B 563 TYR 0.010 0.001 TYR B 319 ARG 0.002 0.000 ARG B 351 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 0.663 Fit side-chains REVERT: B 590 TYR cc_start: 0.8471 (t80) cc_final: 0.7730 (t80) REVERT: B 867 SER cc_start: 0.7784 (m) cc_final: 0.7358 (t) outliers start: 18 outliers final: 11 residues processed: 77 average time/residue: 0.1476 time to fit residues: 16.0030 Evaluate side-chains 73 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain B residue 975 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.4980 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 GLN ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6030 Z= 0.164 Angle : 0.477 9.438 8177 Z= 0.245 Chirality : 0.040 0.134 938 Planarity : 0.003 0.034 1033 Dihedral : 11.002 165.195 907 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 2.45 % Allowed : 13.91 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.61 (0.31), residues: 738 helix: 0.85 (0.28), residues: 362 sheet: 0.49 (0.60), residues: 81 loop : -2.35 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 295 HIS 0.003 0.001 HIS B 300 PHE 0.013 0.001 PHE B 504 TYR 0.019 0.001 TYR B 203 ARG 0.001 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.660 Fit side-chains REVERT: B 590 TYR cc_start: 0.8429 (t80) cc_final: 0.7665 (t80) REVERT: B 867 SER cc_start: 0.7702 (m) cc_final: 0.7280 (t) outliers start: 15 outliers final: 10 residues processed: 71 average time/residue: 0.1371 time to fit residues: 14.3212 Evaluate side-chains 71 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain B residue 975 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 440 GLN B 904 GLN ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6030 Z= 0.289 Angle : 0.542 10.579 8177 Z= 0.281 Chirality : 0.042 0.136 938 Planarity : 0.003 0.033 1033 Dihedral : 11.210 168.216 907 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.81 % Favored : 91.06 % Rotamer: Outliers : 2.29 % Allowed : 13.75 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.77 (0.31), residues: 738 helix: 0.66 (0.28), residues: 362 sheet: 0.18 (0.60), residues: 83 loop : -2.28 (0.33), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 266 HIS 0.007 0.001 HIS B 300 PHE 0.016 0.002 PHE B 563 TYR 0.011 0.001 TYR B 319 ARG 0.002 0.000 ARG B1032 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.705 Fit side-chains REVERT: B 590 TYR cc_start: 0.8476 (t80) cc_final: 0.7709 (t80) REVERT: B 867 SER cc_start: 0.7764 (m) cc_final: 0.7357 (t) outliers start: 14 outliers final: 10 residues processed: 70 average time/residue: 0.1411 time to fit residues: 14.3666 Evaluate side-chains 71 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain B residue 975 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 904 GLN ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6030 Z= 0.262 Angle : 0.524 10.223 8177 Z= 0.271 Chirality : 0.042 0.136 938 Planarity : 0.003 0.034 1033 Dihedral : 11.182 168.675 907 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.81 % Favored : 91.06 % Rotamer: Outliers : 2.29 % Allowed : 14.40 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.83 (0.31), residues: 738 helix: 0.59 (0.28), residues: 362 sheet: 0.14 (0.59), residues: 82 loop : -2.26 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 266 HIS 0.006 0.001 HIS B 300 PHE 0.013 0.002 PHE B 563 TYR 0.021 0.001 TYR B 203 ARG 0.002 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.648 Fit side-chains REVERT: B 590 TYR cc_start: 0.8480 (t80) cc_final: 0.7701 (t80) REVERT: B 867 SER cc_start: 0.7733 (m) cc_final: 0.7333 (t) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.1411 time to fit residues: 14.3764 Evaluate side-chains 70 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain B residue 975 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6030 Z= 0.252 Angle : 0.528 10.148 8177 Z= 0.272 Chirality : 0.041 0.136 938 Planarity : 0.003 0.034 1033 Dihedral : 11.115 169.122 907 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.67 % Favored : 91.19 % Rotamer: Outliers : 2.45 % Allowed : 14.57 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.91 (0.31), residues: 738 helix: 0.46 (0.28), residues: 371 sheet: 0.13 (0.59), residues: 81 loop : -2.29 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 266 HIS 0.006 0.001 HIS B 300 PHE 0.013 0.001 PHE B 563 TYR 0.009 0.001 TYR B 319 ARG 0.002 0.000 ARG B1032 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.699 Fit side-chains REVERT: B 590 TYR cc_start: 0.8478 (t80) cc_final: 0.7700 (t80) REVERT: B 867 SER cc_start: 0.7707 (m) cc_final: 0.7311 (t) outliers start: 15 outliers final: 14 residues processed: 70 average time/residue: 0.1430 time to fit residues: 14.6141 Evaluate side-chains 74 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 387 GLN Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 885 GLU Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 987 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 67 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 0.0020 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 6030 Z= 0.145 Angle : 0.473 9.659 8177 Z= 0.241 Chirality : 0.039 0.134 938 Planarity : 0.003 0.036 1033 Dihedral : 10.799 170.468 907 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.99 % Favored : 91.87 % Rotamer: Outliers : 1.96 % Allowed : 15.06 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.54 (0.31), residues: 738 helix: 0.97 (0.29), residues: 358 sheet: 0.33 (0.59), residues: 81 loop : -2.29 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 295 HIS 0.003 0.001 HIS B 300 PHE 0.011 0.001 PHE B 281 TYR 0.019 0.001 TYR B 203 ARG 0.001 0.000 ARG B 502 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1476 Ramachandran restraints generated. 738 Oldfield, 0 Emsley, 738 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.660 Fit side-chains REVERT: B 590 TYR cc_start: 0.8421 (t80) cc_final: 0.7637 (t80) REVERT: B 867 SER cc_start: 0.7602 (m) cc_final: 0.7203 (t) outliers start: 12 outliers final: 10 residues processed: 71 average time/residue: 0.1503 time to fit residues: 15.5830 Evaluate side-chains 72 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 337 ASP Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 429 ASP Chi-restraints excluded: chain B residue 490 ASN Chi-restraints excluded: chain B residue 975 THR Chi-restraints excluded: chain B residue 987 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 58 optimal weight: 0.0770 chunk 24 optimal weight: 0.0770 chunk 60 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 965 HIS ** 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 = 0.3530 r_free = 0.3530 target = 0.130215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.105332 restraints weight = 7457.806| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.00 r_work: 0.3065 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6030 Z= 0.187 Angle : 0.498 11.167 8177 Z= 0.253 Chirality : 0.040 0.135 938 Planarity : 0.003 0.035 1033 Dihedral : 10.791 171.066 907 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.27 % Favored : 91.60 % Rotamer: Outliers : 2.29 % Allowed : 15.06 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: -0.54 (0.31), residues: 738 helix: 0.96 (0.29), residues: 358 sheet: 0.38 (0.59), residues: 81 loop : -2.29 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 295 HIS 0.004 0.001 HIS B 300 PHE 0.011 0.001 PHE B 504 TYR 0.007 0.001 TYR B 319 ARG 0.002 0.000 ARG B 502 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1503.29 seconds wall clock time: 27 minutes 50.48 seconds (1670.48 seconds total)