Starting phenix.real_space_refine on Wed Feb 14 13:22:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsr_32765/02_2024/7wsr_32765.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsr_32765/02_2024/7wsr_32765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsr_32765/02_2024/7wsr_32765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsr_32765/02_2024/7wsr_32765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsr_32765/02_2024/7wsr_32765.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wsr_32765/02_2024/7wsr_32765.pdb" } resolution = 2.9 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= -0.003 sd= 0.061 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 6268 2.51 5 N 1446 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9366 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4613 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 29, 'TRANS': 570} Chain breaks: 1 Chain: "B" Number of atoms: 4613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4613 Classifications: {'peptide': 600} Link IDs: {'PTRANS': 29, 'TRANS': 570} Chain breaks: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'Y01': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.48, per 1000 atoms: 0.59 Number of scatterers: 9366 At special positions: 0 Unit cell: (101.905, 138.359, 82.0215, 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 74 16.00 O 1578 8.00 N 1446 7.00 C 6268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 250 " - pdb=" SG CYS B 671 " distance=2.03 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: 3.86 Conformation dependent library (CDL) restraints added in 1.7 seconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2152 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 1 sheets defined 78.7% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 50 through 75 Processing helix chain 'A' and resid 81 through 104 removed outlier: 3.642A pdb=" N ALA A 86 " --> pdb=" O ASN A 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 132 removed outlier: 3.541A pdb=" N TYR A 126 " --> pdb=" O GLY A 122 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE A 130 " --> pdb=" O TYR A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 141 removed outlier: 3.651A pdb=" N LEU A 141 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 3.576A pdb=" N GLY A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 191 removed outlier: 4.256A pdb=" N PHE A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLY A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY A 179 " --> pdb=" O CYS A 175 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU A 181 " --> pdb=" O PHE A 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 182 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ILE A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 3.982A pdb=" N GLN A 188 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 213 Processing helix chain 'A' and resid 219 through 243 removed outlier: 3.564A pdb=" N TYR A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 265 Processing helix chain 'A' and resid 272 through 281 removed outlier: 3.915A pdb=" N ILE A 281 " --> pdb=" O GLY A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 299 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 359 removed outlier: 3.674A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 416 removed outlier: 3.927A pdb=" N TYR A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 420 through 446 removed outlier: 3.731A pdb=" N VAL A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.553A pdb=" N LEU A 444 " --> pdb=" O TYR A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 Processing helix chain 'A' and resid 470 through 501 removed outlier: 3.539A pdb=" N GLN A 493 " --> pdb=" O ALA A 489 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP A 494 " --> pdb=" O ASP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 534 removed outlier: 3.562A pdb=" N ILE A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 545 through 560 removed outlier: 3.936A pdb=" N LEU A 549 " --> pdb=" O ALA A 545 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 565 Processing helix chain 'A' and resid 568 through 590 removed outlier: 3.639A pdb=" N ASP A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 removed outlier: 3.801A pdb=" N VAL A 606 " --> pdb=" O MET A 602 " (cutoff:3.500A) Proline residue: A 607 - end of helix removed outlier: 3.561A pdb=" N VAL A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 632 Processing helix chain 'A' and resid 632 through 664 removed outlier: 4.154A pdb=" N PHE A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL A 640 " --> pdb=" O ALA A 636 " (cutoff:3.500A) Proline residue: A 641 - end of helix removed outlier: 3.508A pdb=" N THR A 655 " --> pdb=" O ASP A 651 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE A 656 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Proline residue: A 657 - end of helix Processing helix chain 'B' and resid 50 through 75 Processing helix chain 'B' and resid 81 through 104 removed outlier: 3.642A pdb=" N ALA B 86 " --> pdb=" O ASN B 82 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 132 removed outlier: 3.540A pdb=" N TYR B 126 " --> pdb=" O GLY B 122 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ILE B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA B 129 " --> pdb=" O CYS B 125 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE B 130 " --> pdb=" O TYR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 141 removed outlier: 3.651A pdb=" N LEU B 141 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 150 removed outlier: 3.575A pdb=" N GLY B 150 " --> pdb=" O TYR B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 191 removed outlier: 4.256A pdb=" N PHE B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLY B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLY B 179 " --> pdb=" O CYS B 175 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU B 181 " --> pdb=" O PHE B 177 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 3.980A pdb=" N GLN B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 213 Processing helix chain 'B' and resid 219 through 243 removed outlier: 3.565A pdb=" N TYR B 230 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 265 Processing helix chain 'B' and resid 272 through 281 removed outlier: 3.914A pdb=" N ILE B 281 " --> pdb=" O GLY B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 299 Processing helix chain 'B' and resid 300 through 306 Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 359 removed outlier: 3.674A pdb=" N LYS B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N TYR B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 416 removed outlier: 3.927A pdb=" N TYR B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) Proline residue: B 413 - end of helix Processing helix chain 'B' and resid 420 through 446 removed outlier: 3.732A pdb=" N VAL B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.553A pdb=" N LEU B 444 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 464 Processing helix chain 'B' and resid 470 through 501 removed outlier: 3.539A pdb=" N GLN B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP B 494 " --> pdb=" O ASP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 534 removed outlier: 3.563A pdb=" N ILE B 521 " --> pdb=" O ALA B 517 " (cutoff:3.500A) Proline residue: B 524 - end of helix Processing helix chain 'B' and resid 545 through 560 removed outlier: 3.936A pdb=" N LEU B 549 " --> pdb=" O ALA B 545 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLU B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 565 Processing helix chain 'B' and resid 568 through 590 removed outlier: 3.639A pdb=" N ASP B 588 " --> pdb=" O SER B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 610 removed outlier: 3.801A pdb=" N VAL B 606 " --> pdb=" O MET B 602 " (cutoff:3.500A) Proline residue: B 607 - end of helix removed outlier: 3.561A pdb=" N VAL B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 632 Processing helix chain 'B' and resid 632 through 664 removed outlier: 4.153A pdb=" N PHE B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL B 640 " --> pdb=" O ALA B 636 " (cutoff:3.500A) Proline residue: B 641 - end of helix removed outlier: 3.508A pdb=" N THR B 655 " --> pdb=" O ASP B 651 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 656 " --> pdb=" O GLY B 652 " (cutoff:3.500A) Proline residue: B 657 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 671 through 675 640 hydrogen bonds defined for protein. 1896 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: 2.62 Time building geometry restraints manager: 4.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2720 1.35 - 1.47: 2551 1.47 - 1.58: 4245 1.58 - 1.70: 0 1.70 - 1.82: 126 Bond restraints: 9642 Sorted by residual: bond pdb=" CAI Y01 A 802 " pdb=" CAK Y01 A 802 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CAI Y01 B 701 " pdb=" CAK Y01 B 701 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CAI Y01 B 702 " pdb=" CAK Y01 B 702 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CAI Y01 A 801 " pdb=" CAK Y01 A 801 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" CAI Y01 B 701 " pdb=" CAZ Y01 B 701 " ideal model delta sigma weight residual 1.332 1.382 -0.050 2.00e-02 2.50e+03 6.28e+00 ... (remaining 9637 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.22: 326 106.22 - 113.21: 5136 113.21 - 120.19: 3416 120.19 - 127.18: 4119 127.18 - 134.16: 125 Bond angle restraints: 13122 Sorted by residual: angle pdb=" OAG Y01 A 802 " pdb=" CAY Y01 A 802 " pdb=" OAW Y01 A 802 " ideal model delta sigma weight residual 123.38 111.36 12.02 3.00e+00 1.11e-01 1.61e+01 angle pdb=" OAG Y01 B 701 " pdb=" CAY Y01 B 701 " pdb=" OAW Y01 B 701 " ideal model delta sigma weight residual 123.38 111.37 12.01 3.00e+00 1.11e-01 1.60e+01 angle pdb=" OAG Y01 B 702 " pdb=" CAY Y01 B 702 " pdb=" OAW Y01 B 702 " ideal model delta sigma weight residual 123.38 111.51 11.87 3.00e+00 1.11e-01 1.56e+01 angle pdb=" OAG Y01 A 801 " pdb=" CAY Y01 A 801 " pdb=" OAW Y01 A 801 " ideal model delta sigma weight residual 123.38 111.53 11.85 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CAM Y01 B 701 " pdb=" CAY Y01 B 701 " pdb=" OAW Y01 B 701 " ideal model delta sigma weight residual 111.19 123.01 -11.82 3.00e+00 1.11e-01 1.55e+01 ... (remaining 13117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.38: 5427 16.38 - 32.77: 215 32.77 - 49.15: 70 49.15 - 65.54: 16 65.54 - 81.92: 2 Dihedral angle restraints: 5730 sinusoidal: 2324 harmonic: 3406 Sorted by residual: dihedral pdb=" CB CYS A 250 " pdb=" SG CYS A 250 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -117.84 31.84 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CB CYS B 250 " pdb=" SG CYS B 250 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -117.83 31.83 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CA MET A 322 " pdb=" CB MET A 322 " pdb=" CG MET A 322 " pdb=" SD MET A 322 " ideal model delta sinusoidal sigma weight residual -60.00 -115.05 55.05 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 5727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1157 0.044 - 0.088: 263 0.088 - 0.133: 54 0.133 - 0.177: 6 0.177 - 0.221: 6 Chirality restraints: 1486 Sorted by residual: chirality pdb=" CBF Y01 A 801 " pdb=" CAS Y01 A 801 " pdb=" CBD Y01 A 801 " pdb=" CBH Y01 A 801 " both_signs ideal model delta sigma weight residual False -2.45 -2.67 0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CBF Y01 B 702 " pdb=" CAS Y01 B 702 " pdb=" CBD Y01 B 702 " pdb=" CBH Y01 B 702 " both_signs ideal model delta sigma weight residual False -2.45 -2.66 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CBG Y01 A 802 " pdb=" CAQ Y01 A 802 " pdb=" CBD Y01 A 802 " pdb=" CBI Y01 A 802 " both_signs ideal model delta sigma weight residual False -2.33 -2.52 0.19 2.00e-01 2.50e+01 8.98e-01 ... (remaining 1483 not shown) Planarity restraints: 1576 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 606 " -0.019 5.00e-02 4.00e+02 2.89e-02 1.33e+00 pdb=" N PRO B 607 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO B 607 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 607 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 606 " 0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 607 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 156 " -0.018 5.00e-02 4.00e+02 2.66e-02 1.13e+00 pdb=" N PRO B 157 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " -0.015 5.00e-02 4.00e+02 ... (remaining 1573 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1980 2.78 - 3.31: 9367 3.31 - 3.84: 15499 3.84 - 4.37: 18913 4.37 - 4.90: 32771 Nonbonded interactions: 78530 Sorted by model distance: nonbonded pdb=" O VAL A 123 " pdb=" OG1 THR A 127 " model vdw 2.244 2.440 nonbonded pdb=" O VAL B 123 " pdb=" OG1 THR B 127 " model vdw 2.246 2.440 nonbonded pdb=" OD1 ASP A 446 " pdb=" NE2 GLN A 493 " model vdw 2.246 2.520 nonbonded pdb=" OD1 ASP B 446 " pdb=" NE2 GLN B 493 " model vdw 2.246 2.520 nonbonded pdb=" OH TYR A 328 " pdb=" O LYS A 567 " model vdw 2.311 2.440 ... (remaining 78525 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 3.000 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: 13.480 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.280 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 0.087 9642 Z= 0.243 Angle : 0.646 12.024 13122 Z= 0.295 Chirality : 0.040 0.221 1486 Planarity : 0.003 0.029 1576 Dihedral : 10.320 81.919 3572 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.83 % Allowed : 2.49 % Favored : 96.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.24), residues: 1192 helix: 1.70 (0.17), residues: 850 sheet: None (None), residues: 0 loop : -0.72 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 167 HIS 0.001 0.001 HIS A 212 PHE 0.006 0.001 PHE B 110 TYR 0.007 0.001 TYR A 422 ARG 0.002 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 0.926 Fit side-chains REVERT: A 111 THR cc_start: 0.8030 (p) cc_final: 0.7715 (t) REVERT: A 506 LYS cc_start: 0.7162 (pttp) cc_final: 0.6923 (ptmt) REVERT: A 633 LYS cc_start: 0.8486 (tptm) cc_final: 0.8200 (tptt) REVERT: B 111 THR cc_start: 0.8036 (p) cc_final: 0.7721 (t) REVERT: B 506 LYS cc_start: 0.7160 (pttp) cc_final: 0.6926 (ptmt) REVERT: B 633 LYS cc_start: 0.8486 (tptm) cc_final: 0.8200 (tptt) outliers start: 8 outliers final: 2 residues processed: 196 average time/residue: 0.9641 time to fit residues: 205.0445 Evaluate side-chains 138 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 192 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 70 optimal weight: 0.0470 chunk 108 optimal weight: 2.9990 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9642 Z= 0.214 Angle : 0.554 6.196 13122 Z= 0.279 Chirality : 0.040 0.157 1486 Planarity : 0.004 0.031 1576 Dihedral : 7.524 53.103 1564 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.91 % Allowed : 10.81 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.25), residues: 1192 helix: 2.14 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -0.41 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 PHE 0.018 0.002 PHE A 534 TYR 0.011 0.001 TYR B 126 ARG 0.001 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.019 Fit side-chains REVERT: A 396 MET cc_start: 0.6958 (mpp) cc_final: 0.6170 (tmt) REVERT: A 453 TYR cc_start: 0.8283 (m-10) cc_final: 0.8012 (m-10) REVERT: A 509 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5509 (ttp) REVERT: A 633 LYS cc_start: 0.8105 (tptm) cc_final: 0.7871 (tptt) REVERT: B 396 MET cc_start: 0.6969 (mpp) cc_final: 0.6169 (tmt) REVERT: B 453 TYR cc_start: 0.8281 (m-10) cc_final: 0.8013 (m-10) REVERT: B 509 MET cc_start: 0.5937 (OUTLIER) cc_final: 0.5508 (ttp) REVERT: B 633 LYS cc_start: 0.8084 (tptm) cc_final: 0.7846 (tptt) outliers start: 28 outliers final: 4 residues processed: 158 average time/residue: 1.0461 time to fit residues: 178.4928 Evaluate side-chains 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 634 LYS Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 634 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 87 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9642 Z= 0.159 Angle : 0.511 7.764 13122 Z= 0.253 Chirality : 0.038 0.121 1486 Planarity : 0.004 0.033 1576 Dihedral : 7.209 51.678 1564 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.70 % Allowed : 13.31 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.25), residues: 1192 helix: 2.24 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.43 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 PHE 0.019 0.001 PHE A 638 TYR 0.011 0.001 TYR B 594 ARG 0.001 0.000 ARG B 552 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 135 time to evaluate : 1.092 Fit side-chains REVERT: A 396 MET cc_start: 0.6912 (mpp) cc_final: 0.6081 (tmt) REVERT: A 591 PRO cc_start: 0.7062 (Cg_exo) cc_final: 0.6832 (Cg_endo) REVERT: B 396 MET cc_start: 0.6924 (mpp) cc_final: 0.6082 (tmt) REVERT: B 591 PRO cc_start: 0.7058 (Cg_exo) cc_final: 0.6827 (Cg_endo) outliers start: 26 outliers final: 8 residues processed: 151 average time/residue: 1.1223 time to fit residues: 182.3686 Evaluate side-chains 143 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 135 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 197 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.1980 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.0040 chunk 109 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 57 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9642 Z= 0.157 Angle : 0.506 8.410 13122 Z= 0.249 Chirality : 0.038 0.117 1486 Planarity : 0.004 0.035 1576 Dihedral : 6.993 48.168 1564 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.70 % Allowed : 14.03 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.25), residues: 1192 helix: 2.30 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 654 HIS 0.002 0.001 HIS B 212 PHE 0.018 0.001 PHE A 638 TYR 0.010 0.001 TYR B 126 ARG 0.002 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 0.986 Fit side-chains REVERT: A 396 MET cc_start: 0.6857 (mpp) cc_final: 0.6052 (tmt) REVERT: A 453 TYR cc_start: 0.8126 (m-10) cc_final: 0.7879 (m-80) REVERT: A 509 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5070 (ttt) REVERT: B 396 MET cc_start: 0.6873 (mpp) cc_final: 0.6054 (tmt) REVERT: B 453 TYR cc_start: 0.8124 (m-10) cc_final: 0.7876 (m-80) REVERT: B 509 MET cc_start: 0.5744 (OUTLIER) cc_final: 0.5079 (ttt) outliers start: 26 outliers final: 8 residues processed: 162 average time/residue: 1.1099 time to fit residues: 194.0926 Evaluate side-chains 144 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 134 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 509 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 86 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 59 optimal weight: 0.0050 chunk 104 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9642 Z= 0.177 Angle : 0.520 8.205 13122 Z= 0.256 Chirality : 0.038 0.118 1486 Planarity : 0.004 0.035 1576 Dihedral : 6.904 44.368 1564 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.01 % Allowed : 14.24 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.25), residues: 1192 helix: 2.24 (0.18), residues: 866 sheet: None (None), residues: 0 loop : -0.38 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 654 HIS 0.002 0.001 HIS B 344 PHE 0.014 0.001 PHE A 638 TYR 0.012 0.001 TYR B 343 ARG 0.002 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 0.923 Fit side-chains REVERT: A 396 MET cc_start: 0.6847 (mpp) cc_final: 0.6068 (tmt) REVERT: A 453 TYR cc_start: 0.8153 (m-10) cc_final: 0.7875 (m-80) REVERT: B 396 MET cc_start: 0.6862 (mpp) cc_final: 0.6072 (tmt) REVERT: B 453 TYR cc_start: 0.8155 (m-10) cc_final: 0.7875 (m-80) outliers start: 29 outliers final: 13 residues processed: 167 average time/residue: 1.2204 time to fit residues: 218.6924 Evaluate side-chains 156 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 143 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 498 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 0.3980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9642 Z= 0.235 Angle : 0.558 8.771 13122 Z= 0.276 Chirality : 0.040 0.125 1486 Planarity : 0.004 0.038 1576 Dihedral : 7.041 46.128 1564 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.70 % Allowed : 16.22 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.25), residues: 1192 helix: 2.06 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -0.48 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 167 HIS 0.002 0.001 HIS B 344 PHE 0.019 0.002 PHE B 638 TYR 0.011 0.001 TYR B 244 ARG 0.002 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.255 Fit side-chains REVERT: A 396 MET cc_start: 0.6801 (mpp) cc_final: 0.6033 (tmt) REVERT: A 453 TYR cc_start: 0.8200 (m-10) cc_final: 0.7939 (m-80) REVERT: A 509 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.4991 (ttt) REVERT: B 396 MET cc_start: 0.6816 (mpp) cc_final: 0.6034 (tmt) REVERT: B 453 TYR cc_start: 0.8197 (m-10) cc_final: 0.7938 (m-80) REVERT: B 509 MET cc_start: 0.5681 (OUTLIER) cc_final: 0.4995 (ttt) outliers start: 26 outliers final: 13 residues processed: 165 average time/residue: 1.1420 time to fit residues: 202.3495 Evaluate side-chains 157 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 142 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.1980 chunk 13 optimal weight: 0.0270 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 97 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9642 Z= 0.168 Angle : 0.529 8.632 13122 Z= 0.261 Chirality : 0.038 0.122 1486 Planarity : 0.004 0.036 1576 Dihedral : 6.824 45.576 1564 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.33 % Allowed : 16.11 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.25), residues: 1192 helix: 2.11 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -0.39 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 654 HIS 0.002 0.001 HIS B 212 PHE 0.017 0.001 PHE A 638 TYR 0.010 0.001 TYR B 146 ARG 0.002 0.000 ARG B 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 1.051 Fit side-chains REVERT: A 396 MET cc_start: 0.6767 (mpp) cc_final: 0.6015 (tmt) REVERT: A 453 TYR cc_start: 0.8137 (m-10) cc_final: 0.7857 (m-80) REVERT: A 509 MET cc_start: 0.5688 (OUTLIER) cc_final: 0.4883 (ttt) REVERT: B 396 MET cc_start: 0.6789 (mpp) cc_final: 0.6026 (tmt) REVERT: B 453 TYR cc_start: 0.8137 (m-10) cc_final: 0.7856 (m-80) REVERT: B 509 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.4869 (ttt) outliers start: 32 outliers final: 13 residues processed: 171 average time/residue: 1.0276 time to fit residues: 189.9227 Evaluate side-chains 155 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 594 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9642 Z= 0.249 Angle : 0.602 10.741 13122 Z= 0.291 Chirality : 0.040 0.138 1486 Planarity : 0.004 0.038 1576 Dihedral : 7.023 46.612 1564 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.29 % Allowed : 18.19 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.25), residues: 1192 helix: 1.96 (0.18), residues: 878 sheet: None (None), residues: 0 loop : -0.47 (0.38), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 160 HIS 0.002 0.001 HIS A 212 PHE 0.013 0.002 PHE A 638 TYR 0.012 0.001 TYR B 146 ARG 0.002 0.000 ARG B 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 142 time to evaluate : 1.123 Fit side-chains REVERT: A 396 MET cc_start: 0.6778 (mpp) cc_final: 0.6039 (tmt) REVERT: A 453 TYR cc_start: 0.8198 (m-10) cc_final: 0.7906 (m-80) REVERT: A 509 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.4921 (ttt) REVERT: B 396 MET cc_start: 0.6792 (mpp) cc_final: 0.6040 (tmt) REVERT: B 453 TYR cc_start: 0.8197 (m-10) cc_final: 0.7904 (m-80) REVERT: B 509 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.4922 (ttt) outliers start: 22 outliers final: 13 residues processed: 153 average time/residue: 1.2292 time to fit residues: 201.7004 Evaluate side-chains 153 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 138 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 509 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 0.0170 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9642 Z= 0.216 Angle : 0.584 10.963 13122 Z= 0.283 Chirality : 0.040 0.152 1486 Planarity : 0.004 0.038 1576 Dihedral : 7.015 52.365 1564 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.29 % Allowed : 18.40 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.25), residues: 1192 helix: 2.03 (0.18), residues: 872 sheet: None (None), residues: 0 loop : -0.53 (0.37), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 160 HIS 0.002 0.001 HIS A 212 PHE 0.012 0.001 PHE A 576 TYR 0.012 0.001 TYR A 146 ARG 0.003 0.000 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.093 Fit side-chains REVERT: A 396 MET cc_start: 0.6754 (mpp) cc_final: 0.6033 (tmt) REVERT: A 453 TYR cc_start: 0.8187 (m-10) cc_final: 0.7905 (m-80) REVERT: A 509 MET cc_start: 0.5735 (OUTLIER) cc_final: 0.4899 (ttt) REVERT: B 396 MET cc_start: 0.6769 (mpp) cc_final: 0.6037 (tmt) REVERT: B 453 TYR cc_start: 0.8185 (m-10) cc_final: 0.7901 (m-80) REVERT: B 509 MET cc_start: 0.5764 (OUTLIER) cc_final: 0.4931 (ttt) outliers start: 22 outliers final: 13 residues processed: 156 average time/residue: 1.1503 time to fit residues: 192.8712 Evaluate side-chains 152 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 137 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 193 ASP Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 509 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 73 optimal weight: 0.0980 chunk 58 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 101 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN A 483 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9642 Z= 0.201 Angle : 0.590 10.686 13122 Z= 0.284 Chirality : 0.040 0.136 1486 Planarity : 0.004 0.037 1576 Dihedral : 7.013 59.765 1564 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.77 % Allowed : 19.33 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.25), residues: 1192 helix: 2.04 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -0.39 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 160 HIS 0.003 0.001 HIS A 212 PHE 0.012 0.001 PHE B 576 TYR 0.010 0.001 TYR B 146 ARG 0.003 0.000 ARG B 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.684 Fit side-chains REVERT: A 396 MET cc_start: 0.6779 (mpp) cc_final: 0.6050 (tmt) REVERT: A 453 TYR cc_start: 0.8178 (m-10) cc_final: 0.7901 (m-80) REVERT: A 509 MET cc_start: 0.5704 (OUTLIER) cc_final: 0.4888 (ttt) REVERT: B 396 MET cc_start: 0.6799 (mpp) cc_final: 0.6057 (tmt) REVERT: B 453 TYR cc_start: 0.8173 (m-10) cc_final: 0.7896 (m-80) REVERT: B 506 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6674 (mtmm) REVERT: B 509 MET cc_start: 0.5743 (OUTLIER) cc_final: 0.4931 (ttt) outliers start: 17 outliers final: 12 residues processed: 147 average time/residue: 1.2036 time to fit residues: 189.8262 Evaluate side-chains 151 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 126 TYR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 594 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 594 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.0040 chunk 83 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN B 223 GLN ** B 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.183617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.149693 restraints weight = 10862.672| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.49 r_work: 0.3495 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9642 Z= 0.247 Angle : 0.614 10.808 13122 Z= 0.296 Chirality : 0.041 0.139 1486 Planarity : 0.004 0.039 1576 Dihedral : 7.005 47.149 1564 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.08 % Allowed : 19.13 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.25), residues: 1192 helix: 1.98 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -0.44 (0.37), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 160 HIS 0.003 0.001 HIS A 212 PHE 0.013 0.002 PHE A 576 TYR 0.011 0.001 TYR B 244 ARG 0.003 0.000 ARG B 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3869.99 seconds wall clock time: 69 minutes 16.48 seconds (4156.48 seconds total)