Starting phenix.real_space_refine (version: dev) on Sun Feb 19 15:01:38 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/02_2023/5fn3_3238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/02_2023/5fn3_3238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/02_2023/5fn3_3238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/02_2023/5fn3_3238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/02_2023/5fn3_3238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fn3_3238/02_2023/5fn3_3238.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.006 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 Process input model Symmetric amino acids flipped Residue "A ARG 52": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A ARG 233": "NH1" <-> "NH2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A ARG 626": "NH1" <-> "NH2" Residue "A ARG 629": "NH1" <-> "NH2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A ARG 652": "NH1" <-> "NH2" Residue "A ARG 657": "NH1" <-> "NH2" Residue "A ARG 659": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 9": "OE1" <-> "OE2" Residue "D GLU 10": "OE1" <-> "OE2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 82": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10291 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 665, 5222 Classifications: {'peptide': 665} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 627} Chain: "B" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2234 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 7, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "C" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1868 Classifications: {'peptide': 243} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 235} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 847 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 120 Classifications: {'peptide': 24} Link IDs: {'TRANS': 23} Time building chain proxies: 5.54, per 1000 atoms: 0.54 Number of scatterers: 10291 At special positions: 0 Unit cell: (92.4, 144.2, 110.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1835 8.00 N 1679 7.00 C 6738 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 62 " distance=2.01 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 159 " distance=2.05 Simple disulfide: pdb=" SG CYS A 195 " - pdb=" SG CYS A 213 " distance=2.04 Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 248 " distance=2.02 Simple disulfide: pdb=" SG CYS A 586 " - pdb=" SG CYS A 620 " distance=2.04 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: 4.21 Conformation dependent library (CDL) restraints added in 1.4 seconds 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2482 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 5 sheets defined 60.4% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 34 through 41 removed outlier: 4.230A pdb=" N ARG A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 removed outlier: 3.691A pdb=" N LEU A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 114 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 185 through 200 removed outlier: 4.181A pdb=" N THR A 189 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 226 through 240 Processing helix chain 'A' and resid 298 through 315 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 381 through 387 removed outlier: 3.514A pdb=" N ASN A 387 " --> pdb=" O VAL A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.586A pdb=" N GLY A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.747A pdb=" N PHE A 430 " --> pdb=" O SER A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 464 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.677A pdb=" N ASN A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 502 Processing helix chain 'A' and resid 514 through 527 Processing helix chain 'A' and resid 531 through 537 Processing helix chain 'A' and resid 539 through 546 removed outlier: 3.941A pdb=" N SER A 544 " --> pdb=" O ASP A 541 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 546 " --> pdb=" O ARG A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 576 removed outlier: 3.627A pdb=" N VAL A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 588 Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 665 through 693 Processing helix chain 'B' and resid 79 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 126 through 156 removed outlier: 3.909A pdb=" N THR B 147 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 148 " --> pdb=" O VAL B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 190 removed outlier: 3.779A pdb=" N LEU B 173 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 178 " --> pdb=" O LEU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 215 Processing helix chain 'B' and resid 218 through 241 Processing helix chain 'B' and resid 242 through 262 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.611A pdb=" N VAL B 393 " --> pdb=" O TYR B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 429 Processing helix chain 'B' and resid 434 through 452 removed outlier: 3.515A pdb=" N SER B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 4.235A pdb=" N PHE B 456 " --> pdb=" O LEU B 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 24 Proline residue: C 16 - end of helix Processing helix chain 'C' and resid 28 through 61 Processing helix chain 'C' and resid 64 through 106 removed outlier: 3.676A pdb=" N GLY C 100 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 141 removed outlier: 5.093A pdb=" N ASN C 136 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE C 137 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 185 removed outlier: 3.624A pdb=" N THR C 159 " --> pdb=" O TYR C 155 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 206 removed outlier: 3.903A pdb=" N LEU C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 235 through 243 removed outlier: 3.713A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU C 243 " --> pdb=" O ILE C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 removed outlier: 3.598A pdb=" N LYS D 11 " --> pdb=" O SER D 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE D 23 " --> pdb=" O TYR D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 37 Processing helix chain 'D' and resid 38 through 44 removed outlier: 4.843A pdb=" N VAL D 44 " --> pdb=" O GLU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 82 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'G' and resid 5 through 13 Processing helix chain 'G' and resid 16 through 24 Processing sheet with id= AA, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.490A pdb=" N CYS A 213 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP A 69 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 53 through 54 Processing sheet with id= AC, first strand: chain 'A' and resid 412 through 414 removed outlier: 3.745A pdb=" N SER A 361 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 365 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 602 through 605 Processing sheet with id= BA, first strand: chain 'B' and resid 193 through 194 removed outlier: 6.842A pdb=" N VAL B 193 " --> pdb=" O PHE D 94 " (cutoff:3.500A) 627 hydrogen bonds defined for protein. 1839 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: 2.87 Time building geometry restraints manager: 4.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1684 1.32 - 1.45: 3051 1.45 - 1.58: 5751 1.58 - 1.71: 10 1.71 - 1.84: 59 Bond restraints: 10555 Sorted by residual: bond pdb=" CA THR B 122 " pdb=" C THR B 122 " ideal model delta sigma weight residual 1.523 1.603 -0.080 1.34e-02 5.57e+03 3.53e+01 bond pdb=" CA LEU B 262 " pdb=" C LEU B 262 " ideal model delta sigma weight residual 1.523 1.591 -0.067 1.34e-02 5.57e+03 2.53e+01 bond pdb=" C ILE C 127 " pdb=" O ILE C 127 " ideal model delta sigma weight residual 1.237 1.290 -0.053 1.13e-02 7.83e+03 2.20e+01 bond pdb=" CA HIS B 214 " pdb=" C HIS B 214 " ideal model delta sigma weight residual 1.522 1.564 -0.042 9.30e-03 1.16e+04 2.07e+01 bond pdb=" N LYS B 429 " pdb=" CA LYS B 429 " ideal model delta sigma weight residual 1.457 1.516 -0.058 1.29e-02 6.01e+03 2.04e+01 ... (remaining 10550 not shown) Histogram of bond angle deviations from ideal: 97.85 - 106.46: 333 106.46 - 115.07: 6567 115.07 - 123.67: 6322 123.67 - 132.28: 1146 132.28 - 140.89: 31 Bond angle restraints: 14399 Sorted by residual: angle pdb=" C ASN A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 120.38 130.82 -10.44 1.03e+00 9.43e-01 1.03e+02 angle pdb=" N PRO A 92 " pdb=" CA PRO A 92 " pdb=" C PRO A 92 " ideal model delta sigma weight residual 110.70 121.52 -10.82 1.22e+00 6.72e-01 7.87e+01 angle pdb=" C THR B 256 " pdb=" CA THR B 256 " pdb=" CB THR B 256 " ideal model delta sigma weight residual 110.88 97.85 13.03 1.57e+00 4.06e-01 6.89e+01 angle pdb=" CA VAL B 87 " pdb=" C VAL B 87 " pdb=" N PRO B 88 " ideal model delta sigma weight residual 120.83 115.96 4.87 6.10e-01 2.69e+00 6.38e+01 angle pdb=" CA PRO B 117 " pdb=" N PRO B 117 " pdb=" CD PRO B 117 " ideal model delta sigma weight residual 112.00 101.66 10.34 1.40e+00 5.10e-01 5.45e+01 ... (remaining 14394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.44: 5493 23.44 - 46.88: 557 46.88 - 70.32: 93 70.32 - 93.77: 17 93.77 - 117.21: 1 Dihedral angle restraints: 6161 sinusoidal: 2316 harmonic: 3845 Sorted by residual: dihedral pdb=" CA GLY B 111 " pdb=" C GLY B 111 " pdb=" N GLN B 112 " pdb=" CA GLN B 112 " ideal model delta harmonic sigma weight residual -180.00 -62.79 -117.21 0 5.00e+00 4.00e-02 5.49e+02 dihedral pdb=" CA PRO B 117 " pdb=" C PRO B 117 " pdb=" N PHE B 118 " pdb=" CA PHE B 118 " ideal model delta harmonic sigma weight residual 180.00 87.92 92.08 0 5.00e+00 4.00e-02 3.39e+02 dihedral pdb=" CA ALA G 17 " pdb=" C ALA G 17 " pdb=" N ALA G 18 " pdb=" CA ALA G 18 " ideal model delta harmonic sigma weight residual 180.00 94.37 85.63 0 5.00e+00 4.00e-02 2.93e+02 ... (remaining 6158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1373 0.120 - 0.241: 250 0.241 - 0.361: 42 0.361 - 0.482: 8 0.482 - 0.602: 5 Chirality restraints: 1678 Sorted by residual: chirality pdb=" CA PRO B 117 " pdb=" N PRO B 117 " pdb=" C PRO B 117 " pdb=" CB PRO B 117 " both_signs ideal model delta sigma weight residual False 2.72 2.12 0.60 2.00e-01 2.50e+01 9.07e+00 chirality pdb=" CA THR B 122 " pdb=" N THR B 122 " pdb=" C THR B 122 " pdb=" CB THR B 122 " both_signs ideal model delta sigma weight residual False 2.53 1.94 0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA PHE A 525 " pdb=" N PHE A 525 " pdb=" C PHE A 525 " pdb=" CB PHE A 525 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.20e+00 ... (remaining 1675 not shown) Planarity restraints: 1792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 559 " 0.082 5.00e-02 4.00e+02 1.26e-01 2.54e+01 pdb=" N PRO A 560 " -0.218 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 155 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LYS B 155 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS B 155 " 0.022 2.00e-02 2.50e+03 pdb=" N TYR B 156 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 210 " -0.056 5.00e-02 4.00e+02 8.47e-02 1.15e+01 pdb=" N PRO A 211 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 211 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 211 " -0.048 5.00e-02 4.00e+02 ... (remaining 1789 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.80: 6 1.80 - 2.57: 96 2.57 - 3.35: 13963 3.35 - 4.12: 25650 4.12 - 4.90: 45649 Nonbonded interactions: 85364 Sorted by model distance: nonbonded pdb=" O ALA G 15 " pdb=" CB ALA G 18 " model vdw 1.021 3.460 nonbonded pdb=" SD MET B 146 " pdb=" O ALA G 23 " model vdw 1.099 3.400 nonbonded pdb=" OH TYR B 115 " pdb=" CA ALA G 19 " model vdw 1.163 3.470 nonbonded pdb=" OH TYR B 115 " pdb=" N ALA G 19 " model vdw 1.283 2.520 nonbonded pdb=" O ALA G 12 " pdb=" CB ALA G 14 " model vdw 1.451 3.460 ... (remaining 85359 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 6738 2.51 5 N 1679 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.540 Check model and map are aligned: 0.160 Process input model: 28.880 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 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 : 0.011 0.100 10555 Z= 0.729 Angle : 1.811 15.892 14399 Z= 1.274 Chirality : 0.102 0.602 1678 Planarity : 0.009 0.126 1792 Dihedral : 18.644 117.206 3664 Min Nonbonded Distance : 1.021 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 3.99 % Allowed : 10.74 % Favored : 85.28 % Rotamer Outliers : 11.34 % Cbeta Deviations : 2.10 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.40 % Twisted Proline : 3.51 % Twisted General : 2.07 % 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: -1.54 (0.21), residues: 1304 helix: 1.17 (0.16), residues: 733 sheet: -3.06 (0.39), residues: 108 loop : -4.37 (0.22), residues: 463 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 264 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 30 residues processed: 341 average time/residue: 0.2099 time to fit residues: 103.8181 Evaluate side-chains 190 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 1.225 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.1071 time to fit residues: 7.3999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 8.9990 chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 ASN ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS A 573 ASN ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN B 464 GLN C 68 GLN C 136 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 ASN ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6131 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 10555 Z= 0.291 Angle : 0.923 17.207 14399 Z= 0.468 Chirality : 0.048 0.317 1678 Planarity : 0.008 0.151 1792 Dihedral : 8.116 62.568 1416 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 18.67 Ramachandran Plot: Outliers : 1.38 % Allowed : 9.20 % Favored : 89.42 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.48 % Twisted Proline : 1.75 % Twisted General : 1.12 % 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: -0.60 (0.24), residues: 1304 helix: 1.78 (0.19), residues: 764 sheet: -2.54 (0.41), residues: 124 loop : -4.11 (0.24), residues: 416 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 213 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 216 average time/residue: 0.1812 time to fit residues: 59.0226 Evaluate side-chains 142 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.139 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 80 optimal weight: 0.5980 chunk 32 optimal weight: 9.9990 chunk 118 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 40 optimal weight: 0.3980 chunk 94 optimal weight: 7.9990 overall best weight: 3.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 ASN A 194 GLN ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6206 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 10555 Z= 0.282 Angle : 0.832 14.726 14399 Z= 0.421 Chirality : 0.045 0.284 1678 Planarity : 0.007 0.130 1792 Dihedral : 7.273 51.932 1416 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 19.45 Ramachandran Plot: Outliers : 1.23 % Allowed : 9.20 % Favored : 89.57 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.72 % 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: -0.70 (0.24), residues: 1304 helix: 1.47 (0.19), residues: 757 sheet: -2.14 (0.43), residues: 114 loop : -3.69 (0.26), residues: 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 183 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 185 average time/residue: 0.1973 time to fit residues: 54.4247 Evaluate side-chains 129 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.276 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.1005 time to fit residues: 1.8283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 20.0000 chunk 88 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 118 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 444 HIS ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 606 GLN ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 10555 Z= 0.284 Angle : 0.790 13.975 14399 Z= 0.401 Chirality : 0.043 0.286 1678 Planarity : 0.007 0.125 1792 Dihedral : 7.005 50.854 1416 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 1.15 % Allowed : 9.05 % Favored : 89.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % Twisted General : 0.56 % 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: -0.66 (0.24), residues: 1304 helix: 1.40 (0.18), residues: 759 sheet: -2.19 (0.44), residues: 114 loop : -3.47 (0.27), residues: 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2010 time to fit residues: 51.8079 Evaluate side-chains 121 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.223 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 51 optimal weight: 8.9990 chunk 107 optimal weight: 0.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 HIS A 379 HIS A 428 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN A 610 HIS ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 GLN ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.5461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.063 10555 Z= 0.314 Angle : 0.793 13.663 14399 Z= 0.404 Chirality : 0.043 0.258 1678 Planarity : 0.006 0.103 1792 Dihedral : 6.737 50.097 1416 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 22.12 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.13 % Favored : 89.88 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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 (0.23), residues: 1304 helix: 1.25 (0.18), residues: 749 sheet: -2.06 (0.45), residues: 119 loop : -3.27 (0.27), residues: 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.1891 time to fit residues: 47.7855 Evaluate side-chains 127 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.294 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 0.6980 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.5736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 10555 Z= 0.351 Angle : 0.820 14.608 14399 Z= 0.414 Chirality : 0.044 0.296 1678 Planarity : 0.007 0.151 1792 Dihedral : 6.749 49.397 1416 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 24.06 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.51 % Favored : 89.49 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 3.51 % Twisted General : 0.48 % 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: -0.97 (0.23), residues: 1304 helix: 1.04 (0.18), residues: 744 sheet: -2.29 (0.42), residues: 119 loop : -3.22 (0.28), residues: 441 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1902 time to fit residues: 47.2081 Evaluate side-chains 124 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 1.357 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 77 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 10555 Z= 0.345 Angle : 0.820 13.105 14399 Z= 0.419 Chirality : 0.044 0.276 1678 Planarity : 0.007 0.128 1792 Dihedral : 6.649 48.611 1416 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 24.30 Ramachandran Plot: Outliers : 1.00 % Allowed : 9.97 % Favored : 89.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % Twisted General : 0.40 % 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: -0.99 (0.23), residues: 1304 helix: 1.03 (0.18), residues: 741 sheet: -2.44 (0.41), residues: 119 loop : -3.17 (0.28), residues: 444 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1871 time to fit residues: 46.2641 Evaluate side-chains 120 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 1.146 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A 428 GLN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.6236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 10555 Z= 0.261 Angle : 0.793 13.850 14399 Z= 0.398 Chirality : 0.043 0.190 1678 Planarity : 0.005 0.064 1792 Dihedral : 6.625 46.500 1416 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 22.17 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.89 % Favored : 89.19 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % Twisted General : 0.32 % 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: -0.84 (0.23), residues: 1304 helix: 1.09 (0.18), residues: 734 sheet: -2.36 (0.43), residues: 112 loop : -2.91 (0.28), residues: 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1854 time to fit residues: 47.2866 Evaluate side-chains 128 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 7.9990 chunk 116 optimal weight: 20.0000 chunk 120 optimal weight: 6.9990 chunk 70 optimal weight: 0.0570 chunk 50 optimal weight: 8.9990 chunk 91 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 105 optimal weight: 8.9990 chunk 110 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6304 moved from start: 0.6385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 10555 Z= 0.215 Angle : 0.769 14.561 14399 Z= 0.384 Chirality : 0.043 0.214 1678 Planarity : 0.005 0.064 1792 Dihedral : 6.351 44.728 1416 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.92 % Allowed : 9.28 % Favored : 89.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % Twisted General : 0.32 % 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: -0.76 (0.23), residues: 1304 helix: 1.08 (0.18), residues: 736 sheet: -2.30 (0.44), residues: 112 loop : -2.76 (0.29), residues: 456 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1870 time to fit residues: 50.3189 Evaluate side-chains 123 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 1.165 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 129 optimal weight: 40.0000 chunk 119 optimal weight: 9.9990 chunk 103 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 79 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 562 ASN A 573 ASN ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.075 10555 Z= 0.308 Angle : 0.805 14.721 14399 Z= 0.407 Chirality : 0.043 0.214 1678 Planarity : 0.005 0.064 1792 Dihedral : 6.361 44.363 1416 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.92 % Allowed : 10.51 % Favored : 88.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 1.75 % Twisted General : 0.32 % 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: -0.90 (0.23), residues: 1304 helix: 0.97 (0.18), residues: 736 sheet: -2.37 (0.44), residues: 112 loop : -2.82 (0.29), residues: 456 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2608 Ramachandran restraints generated. 1304 Oldfield, 0 Emsley, 1304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1802 time to fit residues: 44.4091 Evaluate side-chains 122 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 199 HIS A 428 GLN ** A 530 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 535 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.048139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.041864 restraints weight = 76414.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.042775 restraints weight = 51037.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.043459 restraints weight = 37941.235| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.6685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 10555 Z= 0.233 Angle : 0.782 15.469 14399 Z= 0.386 Chirality : 0.042 0.216 1678 Planarity : 0.005 0.063 1792 Dihedral : 6.130 43.204 1416 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.84 % Allowed : 9.05 % Favored : 90.11 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.56 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -0.81 (0.23), residues: 1304 helix: 1.06 (0.18), residues: 737 sheet: -2.34 (0.44), residues: 112 loop : -2.83 (0.29), residues: 455 =============================================================================== Job complete usr+sys time: 1884.34 seconds wall clock time: 35 minutes 51.33 seconds (2151.33 seconds total)