Starting phenix.real_space_refine on Tue Feb 13 23:27:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/02_2024/7zt6_14955_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/02_2024/7zt6_14955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/02_2024/7zt6_14955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/02_2024/7zt6_14955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/02_2024/7zt6_14955_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zt6_14955/02_2024/7zt6_14955_updated.pdb" } resolution = 3.5 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 38 5.16 5 C 5175 2.51 5 N 1363 2.21 5 O 1491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 441": "OD1" <-> "OD2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 428": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8073 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3863 Classifications: {'peptide': 501} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 27, 'TRANS': 473} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 225 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 130 Chain: "B" Number of atoms: 4174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 4174 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 26, 'TRANS': 503} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.88, per 1000 atoms: 0.60 Number of scatterers: 8073 At special positions: 0 Unit cell: (88.02, 92.584, 132.356, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 6 15.00 O 1491 8.00 N 1363 7.00 C 5175 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.8 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1970 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 7 sheets defined 32.0% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 59 through 77 Processing helix chain 'A' and resid 113 through 122 removed outlier: 4.075A pdb=" N PHE A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 134 Processing helix chain 'A' and resid 143 through 155 Processing helix chain 'A' and resid 180 through 196 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 239 through 250 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 331 through 337 Processing helix chain 'A' and resid 378 through 392 Processing helix chain 'A' and resid 456 through 469 Processing helix chain 'A' and resid 481 through 495 Processing helix chain 'A' and resid 511 through 529 removed outlier: 6.496A pdb=" N SER A 520 " --> pdb=" O LYS A 516 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU A 521 " --> pdb=" O ARG A 517 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ASP A 523 " --> pdb=" O GLY A 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 88 through 95 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 200 through 222 removed outlier: 7.834A pdb=" N GLU B 218 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N ASP B 219 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU B 221 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASP B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.982A pdb=" N ARG B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' 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 331 Processing helix chain 'B' and resid 353 through 355 No H-bonds generated for 'chain 'B' and resid 353 through 355' Processing helix chain 'B' and resid 371 through 387 Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 448 through 460 Processing helix chain 'B' and resid 485 through 499 Processing helix chain 'B' and resid 510 through 515 Processing helix chain 'B' and resid 520 through 536 removed outlier: 4.819A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 199 through 204 removed outlier: 3.617A pdb=" N ARG A 165 " --> pdb=" O SER A 37 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU A 82 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N PHE A 40 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ALA A 84 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL A 42 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 86 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 257 through 262 removed outlier: 3.536A pdb=" N TYR A 369 " --> pdb=" O GLY A 272 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR A 409 " --> pdb=" O TYR A 400 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N VAL A 394 " --> pdb=" O PRO A 415 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY A 349 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG A 399 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU A 347 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 318 through 322 Processing sheet with id= D, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.982A pdb=" N GLU B 53 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 10 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 129 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL B 11 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS B 131 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N CYS B 13 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU B 133 " --> pdb=" O CYS B 13 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ASP B 15 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N PHE B 135 " --> pdb=" O ASP B 15 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N SER B 160 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ILE B 134 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLN B 162 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 249 through 253 removed outlier: 3.587A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 361 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.880A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL B 405 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 344 " --> pdb=" O ILE B 392 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ARG B 394 " --> pdb=" O VAL B 342 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL B 342 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA B 396 " --> pdb=" O PHE B 340 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE B 340 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 313 through 316 Processing sheet with id= G, first strand: chain 'B' and resid 464 through 467 removed outlier: 4.481A pdb=" N THR B 472 " --> pdb=" O ASP B 467 " (cutoff:3.500A) 290 hydrogen bonds defined for protein. 846 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: 2.11 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2576 1.34 - 1.46: 1274 1.46 - 1.57: 4319 1.57 - 1.69: 6 1.69 - 1.81: 64 Bond restraints: 8239 Sorted by residual: bond pdb=" O12 IHP A 701 " pdb=" P2 IHP A 701 " ideal model delta sigma weight residual 1.675 1.595 0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" O15 IHP A 701 " pdb=" P5 IHP A 701 " ideal model delta sigma weight residual 1.675 1.598 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" O16 IHP A 701 " pdb=" P6 IHP A 701 " ideal model delta sigma weight residual 1.672 1.603 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C MET A 446 " pdb=" N PRO A 447 " ideal model delta sigma weight residual 1.334 1.371 -0.037 1.11e-02 8.12e+03 1.11e+01 bond pdb=" N ARG A 444 " pdb=" CA ARG A 444 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.18e-02 7.18e+03 9.56e+00 ... (remaining 8234 not shown) Histogram of bond angle deviations from ideal: 98.29 - 105.46: 196 105.46 - 112.62: 4464 112.62 - 119.78: 2509 119.78 - 126.95: 3897 126.95 - 134.11: 83 Bond angle restraints: 11149 Sorted by residual: angle pdb=" N LYS A 358 " pdb=" CA LYS A 358 " pdb=" C LYS A 358 " ideal model delta sigma weight residual 113.41 108.08 5.33 1.22e+00 6.72e-01 1.91e+01 angle pdb=" N VAL B 16 " pdb=" CA VAL B 16 " pdb=" C VAL B 16 " ideal model delta sigma weight residual 111.88 107.28 4.60 1.06e+00 8.90e-01 1.89e+01 angle pdb=" N LYS B 481 " pdb=" CA LYS B 481 " pdb=" C LYS B 481 " ideal model delta sigma weight residual 113.23 108.09 5.14 1.24e+00 6.50e-01 1.72e+01 angle pdb=" CA ILE B 482 " pdb=" C ILE B 482 " pdb=" O ILE B 482 " ideal model delta sigma weight residual 119.71 115.91 3.80 9.30e-01 1.16e+00 1.67e+01 angle pdb=" CA ILE B 482 " pdb=" C ILE B 482 " pdb=" N PRO B 483 " ideal model delta sigma weight residual 119.15 123.56 -4.41 1.20e+00 6.94e-01 1.35e+01 ... (remaining 11144 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4641 17.56 - 35.12: 352 35.12 - 52.69: 61 52.69 - 70.25: 16 70.25 - 87.81: 6 Dihedral angle restraints: 5076 sinusoidal: 2051 harmonic: 3025 Sorted by residual: dihedral pdb=" CA GLU B 199 " pdb=" C GLU B 199 " pdb=" N GLN B 200 " pdb=" CA GLN B 200 " ideal model delta harmonic sigma weight residual 180.00 156.69 23.31 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA MET B 14 " pdb=" C MET B 14 " pdb=" N ASP B 15 " pdb=" CA ASP B 15 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA LYS A 510 " pdb=" C LYS A 510 " pdb=" N VAL A 511 " pdb=" CA VAL A 511 " ideal model delta harmonic sigma weight residual -180.00 -161.34 -18.66 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 5073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1126 0.074 - 0.148: 134 0.148 - 0.222: 5 0.222 - 0.295: 1 0.295 - 0.369: 1 Chirality restraints: 1267 Sorted by residual: chirality pdb=" C1 IHP A 701 " pdb=" C2 IHP A 701 " pdb=" C6 IHP A 701 " pdb=" O11 IHP A 701 " both_signs ideal model delta sigma weight residual False 2.32 2.69 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" C5 IHP A 701 " pdb=" C4 IHP A 701 " pdb=" C6 IHP A 701 " pdb=" O15 IHP A 701 " both_signs ideal model delta sigma weight residual False -2.42 -2.66 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" C3 IHP A 701 " pdb=" C2 IHP A 701 " pdb=" C4 IHP A 701 " pdb=" O13 IHP A 701 " both_signs ideal model delta sigma weight residual False -2.34 -2.55 0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1264 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 71 " 0.014 2.00e-02 2.50e+03 1.12e-02 2.52e+00 pdb=" CG TYR A 71 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR A 71 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 71 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 71 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 71 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 71 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 71 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 161 " 0.006 2.00e-02 2.50e+03 1.25e-02 1.55e+00 pdb=" C MET A 161 " -0.022 2.00e-02 2.50e+03 pdb=" O MET A 161 " 0.008 2.00e-02 2.50e+03 pdb=" N SER A 162 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 199 " -0.006 2.00e-02 2.50e+03 1.15e-02 1.32e+00 pdb=" C GLU B 199 " 0.020 2.00e-02 2.50e+03 pdb=" O GLU B 199 " -0.007 2.00e-02 2.50e+03 pdb=" N GLN B 200 " -0.007 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 986 2.74 - 3.28: 8771 3.28 - 3.82: 13780 3.82 - 4.36: 15816 4.36 - 4.90: 26387 Nonbonded interactions: 65740 Sorted by model distance: nonbonded pdb=" OD1 ASP B 467 " pdb=" OG1 THR B 472 " model vdw 2.203 2.440 nonbonded pdb=" O ASP B 116 " pdb=" ND1 HIS B 120 " model vdw 2.221 2.520 nonbonded pdb=" OG SER B 348 " pdb=" OD2 ASP B 388 " model vdw 2.229 2.440 nonbonded pdb=" OE2 GLU A 371 " pdb=" OG SER A 373 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR A 361 " pdb=" O GLY B 358 " model vdw 2.236 2.440 ... (remaining 65735 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.590 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: 5.900 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.590 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 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 : 0.006 0.080 8239 Z= 0.393 Angle : 0.707 8.637 11149 Z= 0.389 Chirality : 0.045 0.369 1267 Planarity : 0.003 0.027 1424 Dihedral : 13.206 87.810 3106 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.70 % Allowed : 0.35 % Favored : 98.95 % 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: 0.29 (0.27), residues: 1025 helix: 1.84 (0.29), residues: 328 sheet: -0.65 (0.39), residues: 167 loop : -0.55 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 148 HIS 0.004 0.001 HIS B 131 PHE 0.015 0.001 PHE B 135 TYR 0.028 0.002 TYR A 71 ARG 0.003 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 1.316 Fit side-chains REVERT: A 48 MET cc_start: 0.9190 (mmt) cc_final: 0.8882 (mmm) REVERT: A 62 MET cc_start: 0.9366 (mmp) cc_final: 0.9099 (mmm) REVERT: A 348 MET cc_start: 0.8698 (mpp) cc_final: 0.8205 (mpp) REVERT: A 514 MET cc_start: 0.9723 (ptp) cc_final: 0.9435 (pmm) REVERT: B 13 CYS cc_start: 0.9172 (t) cc_final: 0.8794 (t) REVERT: B 14 MET cc_start: 0.9160 (tpp) cc_final: 0.8933 (tpp) REVERT: B 115 MET cc_start: 0.7604 (ppp) cc_final: 0.7173 (ppp) REVERT: B 479 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8860 (t) outliers start: 6 outliers final: 1 residues processed: 46 average time/residue: 0.2569 time to fit residues: 17.1989 Evaluate side-chains 35 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 33 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 479 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8239 Z= 0.163 Angle : 0.524 7.345 11149 Z= 0.263 Chirality : 0.041 0.141 1267 Planarity : 0.003 0.022 1424 Dihedral : 4.994 51.842 1143 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.81 % Allowed : 5.23 % Favored : 93.95 % 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: 0.48 (0.27), residues: 1025 helix: 1.97 (0.29), residues: 337 sheet: -0.55 (0.40), residues: 165 loop : -0.46 (0.29), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 148 HIS 0.003 0.001 HIS B 131 PHE 0.011 0.001 PHE B 135 TYR 0.016 0.001 TYR A 71 ARG 0.002 0.000 ARG A 244 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 38 time to evaluate : 1.108 Fit side-chains REVERT: A 62 MET cc_start: 0.9377 (mmp) cc_final: 0.9150 (mmm) REVERT: A 203 MET cc_start: 0.9466 (mmm) cc_final: 0.8875 (mmm) REVERT: A 348 MET cc_start: 0.8740 (mpp) cc_final: 0.8149 (mpp) REVERT: A 398 CYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8718 (t) REVERT: B 13 CYS cc_start: 0.9319 (t) cc_final: 0.9099 (t) REVERT: B 115 MET cc_start: 0.7739 (ppp) cc_final: 0.7368 (ppp) REVERT: B 479 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9109 (t) outliers start: 7 outliers final: 2 residues processed: 40 average time/residue: 0.1577 time to fit residues: 10.4957 Evaluate side-chains 37 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 398 CYS Chi-restraints excluded: chain B residue 479 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 chunk 25 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 83 optimal weight: 0.2980 chunk 92 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 8239 Z= 0.116 Angle : 0.496 7.570 11149 Z= 0.245 Chirality : 0.040 0.141 1267 Planarity : 0.003 0.021 1424 Dihedral : 4.558 45.265 1143 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.58 % Allowed : 9.30 % Favored : 90.12 % 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: 0.52 (0.27), residues: 1025 helix: 1.99 (0.29), residues: 336 sheet: -0.43 (0.41), residues: 163 loop : -0.46 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 148 HIS 0.003 0.000 HIS B 131 PHE 0.007 0.001 PHE A 211 TYR 0.013 0.001 TYR A 71 ARG 0.002 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 1.017 Fit side-chains REVERT: A 48 MET cc_start: 0.9241 (mmm) cc_final: 0.8793 (mmm) REVERT: A 62 MET cc_start: 0.9377 (mmp) cc_final: 0.9145 (mmm) REVERT: A 348 MET cc_start: 0.8715 (mpp) cc_final: 0.8196 (mpp) REVERT: A 398 CYS cc_start: 0.9096 (m) cc_final: 0.8699 (t) REVERT: B 115 MET cc_start: 0.7896 (ppp) cc_final: 0.7457 (ppp) REVERT: B 212 MET cc_start: 0.9453 (tpp) cc_final: 0.9239 (tpp) REVERT: B 427 MET cc_start: 0.8458 (mpp) cc_final: 0.8157 (mpp) REVERT: B 434 MET cc_start: 0.9010 (tpp) cc_final: 0.8739 (tpt) REVERT: B 479 THR cc_start: 0.9346 (OUTLIER) cc_final: 0.9082 (t) outliers start: 5 outliers final: 3 residues processed: 43 average time/residue: 0.1512 time to fit residues: 10.7311 Evaluate side-chains 36 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 479 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 527 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8239 Z= 0.338 Angle : 0.564 7.067 11149 Z= 0.281 Chirality : 0.039 0.133 1267 Planarity : 0.003 0.023 1424 Dihedral : 4.533 38.136 1143 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 0.93 % Allowed : 10.93 % Favored : 88.14 % 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: 0.65 (0.28), residues: 1025 helix: 2.11 (0.29), residues: 342 sheet: -0.46 (0.40), residues: 169 loop : -0.37 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 148 HIS 0.004 0.001 HIS B 414 PHE 0.029 0.001 PHE B 135 TYR 0.013 0.001 TYR A 322 ARG 0.005 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 1.048 Fit side-chains REVERT: A 48 MET cc_start: 0.9297 (mmm) cc_final: 0.8482 (mmm) REVERT: A 62 MET cc_start: 0.9430 (mmp) cc_final: 0.9143 (mmm) REVERT: A 348 MET cc_start: 0.8718 (mpp) cc_final: 0.8262 (mpp) REVERT: A 398 CYS cc_start: 0.9054 (m) cc_final: 0.8689 (t) REVERT: B 212 MET cc_start: 0.9530 (tpp) cc_final: 0.9288 (tpp) REVERT: B 479 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9306 (t) outliers start: 8 outliers final: 7 residues processed: 40 average time/residue: 0.1624 time to fit residues: 10.7539 Evaluate side-chains 41 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 33 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 479 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 10.0000 chunk 56 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8239 Z= 0.358 Angle : 0.585 8.705 11149 Z= 0.292 Chirality : 0.039 0.132 1267 Planarity : 0.003 0.023 1424 Dihedral : 4.594 28.013 1143 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.63 % Allowed : 11.28 % Favored : 87.09 % 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: 0.59 (0.27), residues: 1025 helix: 2.03 (0.28), residues: 343 sheet: -0.38 (0.39), residues: 179 loop : -0.43 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 148 HIS 0.005 0.001 HIS B 414 PHE 0.029 0.001 PHE B 135 TYR 0.013 0.001 TYR A 322 ARG 0.003 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 0.978 Fit side-chains REVERT: A 62 MET cc_start: 0.9460 (mmp) cc_final: 0.9128 (mmm) REVERT: A 135 MET cc_start: 0.9296 (mmm) cc_final: 0.8926 (mmm) REVERT: A 167 MET cc_start: 0.9350 (mtp) cc_final: 0.9070 (mtt) REVERT: A 348 MET cc_start: 0.8735 (mpp) cc_final: 0.8268 (mpp) REVERT: A 398 CYS cc_start: 0.9063 (m) cc_final: 0.8697 (t) REVERT: B 14 MET cc_start: 0.9627 (tpp) cc_final: 0.9316 (tpp) REVERT: B 115 MET cc_start: 0.7532 (ppp) cc_final: 0.7135 (ppp) REVERT: B 212 MET cc_start: 0.9577 (tpp) cc_final: 0.9312 (tpp) outliers start: 14 outliers final: 9 residues processed: 45 average time/residue: 0.1857 time to fit residues: 13.3353 Evaluate side-chains 41 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 89 ASP Chi-restraints excluded: chain B residue 351 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 58 optimal weight: 20.0000 chunk 24 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 52 optimal weight: 0.0010 overall best weight: 1.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8239 Z= 0.152 Angle : 0.512 9.002 11149 Z= 0.250 Chirality : 0.039 0.138 1267 Planarity : 0.002 0.020 1424 Dihedral : 4.302 23.574 1142 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.05 % Allowed : 12.09 % Favored : 86.86 % 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: 0.68 (0.27), residues: 1025 helix: 2.16 (0.29), residues: 337 sheet: -0.56 (0.40), residues: 163 loop : -0.31 (0.29), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 148 HIS 0.003 0.001 HIS B 131 PHE 0.021 0.001 PHE B 135 TYR 0.008 0.001 TYR A 71 ARG 0.005 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 33 time to evaluate : 1.049 Fit side-chains REVERT: A 48 MET cc_start: 0.9143 (mmm) cc_final: 0.8554 (mmm) REVERT: A 62 MET cc_start: 0.9433 (mmp) cc_final: 0.9105 (mmm) REVERT: A 135 MET cc_start: 0.9271 (mmm) cc_final: 0.9059 (mmm) REVERT: A 167 MET cc_start: 0.9336 (mtp) cc_final: 0.9064 (mtt) REVERT: A 348 MET cc_start: 0.8747 (mpp) cc_final: 0.8285 (mpp) REVERT: A 398 CYS cc_start: 0.9085 (m) cc_final: 0.8672 (t) REVERT: B 14 MET cc_start: 0.9591 (tpp) cc_final: 0.9325 (tpp) REVERT: B 212 MET cc_start: 0.9563 (tpp) cc_final: 0.9287 (tpp) REVERT: B 357 MET cc_start: 0.8828 (mmm) cc_final: 0.8522 (tpp) outliers start: 9 outliers final: 6 residues processed: 41 average time/residue: 0.1567 time to fit residues: 10.5608 Evaluate side-chains 38 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 55 optimal weight: 0.0970 chunk 99 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 61 optimal weight: 0.0010 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8239 Z= 0.154 Angle : 0.527 10.233 11149 Z= 0.250 Chirality : 0.039 0.138 1267 Planarity : 0.002 0.020 1424 Dihedral : 4.146 23.275 1142 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.05 % Allowed : 13.37 % Favored : 85.58 % 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: 0.71 (0.27), residues: 1025 helix: 2.19 (0.29), residues: 336 sheet: -0.51 (0.40), residues: 163 loop : -0.30 (0.29), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 148 HIS 0.003 0.001 HIS B 131 PHE 0.015 0.001 PHE B 135 TYR 0.009 0.001 TYR A 141 ARG 0.004 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.948 Fit side-chains REVERT: A 48 MET cc_start: 0.9154 (mmm) cc_final: 0.8820 (mmm) REVERT: A 62 MET cc_start: 0.9426 (mmp) cc_final: 0.9089 (mmm) REVERT: A 348 MET cc_start: 0.8729 (mpp) cc_final: 0.8259 (mpp) REVERT: A 398 CYS cc_start: 0.9073 (m) cc_final: 0.8663 (t) REVERT: B 115 MET cc_start: 0.7590 (ppp) cc_final: 0.7214 (ppp) REVERT: B 212 MET cc_start: 0.9579 (tpp) cc_final: 0.9310 (tpp) REVERT: B 357 MET cc_start: 0.8809 (mmm) cc_final: 0.8511 (tpp) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.1556 time to fit residues: 10.7603 Evaluate side-chains 40 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 33 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 407 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 63 optimal weight: 6.9990 chunk 67 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 78 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 500 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8239 Z= 0.128 Angle : 0.544 10.431 11149 Z= 0.256 Chirality : 0.039 0.139 1267 Planarity : 0.002 0.022 1424 Dihedral : 3.975 22.920 1141 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.05 % Allowed : 13.49 % Favored : 85.47 % 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: 0.75 (0.27), residues: 1025 helix: 2.21 (0.29), residues: 336 sheet: -0.43 (0.40), residues: 163 loop : -0.29 (0.28), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 148 HIS 0.002 0.000 HIS B 131 PHE 0.013 0.001 PHE B 135 TYR 0.006 0.001 TYR A 71 ARG 0.002 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 34 time to evaluate : 0.988 Fit side-chains REVERT: A 48 MET cc_start: 0.9114 (mmm) cc_final: 0.8778 (mmm) REVERT: A 62 MET cc_start: 0.9420 (mmp) cc_final: 0.9088 (mmm) REVERT: A 348 MET cc_start: 0.8734 (mpp) cc_final: 0.8267 (mpp) REVERT: A 398 CYS cc_start: 0.9077 (m) cc_final: 0.8678 (t) REVERT: A 511 VAL cc_start: 0.9707 (OUTLIER) cc_final: 0.9504 (p) REVERT: A 514 MET cc_start: 0.9642 (ptp) cc_final: 0.9313 (pmm) REVERT: B 115 MET cc_start: 0.7618 (ppp) cc_final: 0.7167 (ppp) REVERT: B 212 MET cc_start: 0.9570 (tpp) cc_final: 0.9319 (tpp) REVERT: B 223 GLU cc_start: 0.9298 (mt-10) cc_final: 0.9097 (mp0) REVERT: B 357 MET cc_start: 0.8778 (mmm) cc_final: 0.8449 (tpp) outliers start: 9 outliers final: 7 residues processed: 42 average time/residue: 0.1580 time to fit residues: 10.9783 Evaluate side-chains 42 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 407 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 95 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 72 optimal weight: 0.0570 chunk 28 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8239 Z= 0.161 Angle : 0.559 11.431 11149 Z= 0.259 Chirality : 0.039 0.138 1267 Planarity : 0.002 0.020 1424 Dihedral : 3.906 22.061 1141 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.93 % Allowed : 14.07 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.27), residues: 1025 helix: 2.22 (0.29), residues: 338 sheet: -0.30 (0.40), residues: 165 loop : -0.23 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 148 HIS 0.003 0.001 HIS B 131 PHE 0.013 0.001 PHE B 135 TYR 0.006 0.001 TYR A 71 ARG 0.001 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 1.167 Fit side-chains REVERT: A 62 MET cc_start: 0.9415 (mmp) cc_final: 0.9089 (mmm) REVERT: A 167 MET cc_start: 0.9398 (mtp) cc_final: 0.9142 (mtt) REVERT: A 348 MET cc_start: 0.8732 (mpp) cc_final: 0.8302 (mpp) REVERT: A 398 CYS cc_start: 0.9055 (m) cc_final: 0.8660 (t) REVERT: B 58 LEU cc_start: 0.9710 (OUTLIER) cc_final: 0.9348 (tp) REVERT: B 115 MET cc_start: 0.7625 (ppp) cc_final: 0.7178 (ppp) REVERT: B 212 MET cc_start: 0.9569 (tpp) cc_final: 0.9323 (tpp) REVERT: B 357 MET cc_start: 0.8795 (mmm) cc_final: 0.8482 (tpp) outliers start: 8 outliers final: 5 residues processed: 41 average time/residue: 0.1718 time to fit residues: 11.5411 Evaluate side-chains 39 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 33 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 407 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 63 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8239 Z= 0.267 Angle : 0.596 11.757 11149 Z= 0.281 Chirality : 0.039 0.135 1267 Planarity : 0.003 0.021 1424 Dihedral : 4.025 20.701 1141 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.81 % Allowed : 14.30 % Favored : 84.88 % 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: 0.83 (0.28), residues: 1025 helix: 2.22 (0.29), residues: 337 sheet: -0.40 (0.39), residues: 172 loop : -0.18 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 148 HIS 0.003 0.001 HIS B 131 PHE 0.017 0.001 PHE B 135 TYR 0.011 0.001 TYR A 322 ARG 0.002 0.000 ARG B 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.993 Fit side-chains REVERT: A 62 MET cc_start: 0.9423 (mmp) cc_final: 0.9072 (mmm) REVERT: A 167 MET cc_start: 0.9424 (mtp) cc_final: 0.9119 (mtt) REVERT: A 348 MET cc_start: 0.8674 (mpp) cc_final: 0.8282 (mpp) REVERT: A 398 CYS cc_start: 0.9071 (m) cc_final: 0.8671 (t) REVERT: A 514 MET cc_start: 0.9641 (ptp) cc_final: 0.9388 (pmm) REVERT: B 58 LEU cc_start: 0.9720 (OUTLIER) cc_final: 0.9357 (tp) REVERT: B 115 MET cc_start: 0.7609 (ppp) cc_final: 0.7246 (ppp) REVERT: B 212 MET cc_start: 0.9598 (tpp) cc_final: 0.9261 (tpp) REVERT: B 357 MET cc_start: 0.8846 (mmm) cc_final: 0.8563 (tpp) outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 0.1586 time to fit residues: 9.9944 Evaluate side-chains 38 residues out of total 932 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 MET Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 522 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 407 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 8.9990 chunk 75 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 10.0000 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 15 optimal weight: 10.0000 chunk 71 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.046597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.038863 restraints weight = 71675.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.039821 restraints weight = 31884.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.040479 restraints weight = 19164.183| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 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 : 0.005 0.050 8239 Z= 0.300 Angle : 0.615 11.856 11149 Z= 0.291 Chirality : 0.039 0.135 1267 Planarity : 0.003 0.021 1424 Dihedral : 4.149 20.130 1141 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.70 % Allowed : 14.42 % Favored : 84.88 % 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: 0.81 (0.28), residues: 1025 helix: 2.16 (0.29), residues: 343 sheet: -0.35 (0.40), residues: 164 loop : -0.22 (0.30), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 148 HIS 0.004 0.001 HIS B 414 PHE 0.019 0.001 PHE B 135 TYR 0.011 0.001 TYR A 322 ARG 0.002 0.000 ARG B 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1571.37 seconds wall clock time: 29 minutes 42.25 seconds (1782.25 seconds total)