Starting phenix.real_space_refine on Wed Jan 17 23:28:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/01_2024/7u2a_26310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/01_2024/7u2a_26310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/01_2024/7u2a_26310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/01_2024/7u2a_26310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/01_2024/7u2a_26310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/01_2024/7u2a_26310_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 38 5.49 5 S 34 5.16 5 C 4179 2.51 5 N 1233 2.21 5 O 1371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 187": "NH1" <-> "NH2" Residue "A PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A ASP 213": "OD1" <-> "OD2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A GLU 407": "OE1" <-> "OE2" Residue "A ARG 415": "NH1" <-> "NH2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "B TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ARG 82": "NH1" <-> "NH2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B GLU 101": "OE1" <-> "OE2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B GLU 160": "OE1" <-> "OE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ASP 213": "OD1" <-> "OD2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ASP 293": "OD1" <-> "OD2" Residue "B PHE 315": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 316": "NH1" <-> "NH2" Residue "B GLU 332": "OE1" <-> "OE2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B GLU 381": "OE1" <-> "OE2" Residue "B ASP 390": "OD1" <-> "OD2" Residue "B GLU 395": "OE1" <-> "OE2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B GLU 407": "OE1" <-> "OE2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 415": "NH1" <-> "NH2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 427": "OD1" <-> "OD2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B ASP 472": "OD1" <-> "OD2" Residue "B ARG 489": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6855 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 794 Classifications: {'RNA': 38} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 15, 'rna3p_pyr': 20} Link IDs: {'rna2p': 2, 'rna3p': 35} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {' A%rna2p_pur:plan2': 1, ' A%rna2p_pur:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2500 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3503 Classifications: {'peptide': 442} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 415} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SSA%rna3p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 4.47, per 1000 atoms: 0.65 Number of scatterers: 6855 At special positions: 0 Unit cell: (70.15, 83.95, 117.3, 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 34 16.00 P 38 15.00 O 1371 8.00 N 1233 7.00 C 4179 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: 3.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 5 sheets defined 36.7% alpha, 14.8% beta 10 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 205 through 212 Processing helix chain 'A' and resid 221 through 224 No H-bonds generated for 'chain 'A' and resid 221 through 224' Processing helix chain 'A' and resid 234 through 252 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 300 through 307 Processing helix chain 'A' and resid 361 through 382 Processing helix chain 'A' and resid 429 through 433 Processing helix chain 'A' and resid 457 through 467 Processing helix chain 'A' and resid 479 through 485 removed outlier: 4.296A pdb=" N SER A 483 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TYR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 50 Processing helix chain 'B' and resid 60 through 64 Processing helix chain 'B' and resid 67 through 77 Processing helix chain 'B' and resid 83 through 117 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 139 through 169 Proline residue: B 154 - end of helix removed outlier: 4.233A pdb=" N LYS B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 212 Processing helix chain 'B' and resid 221 through 224 No H-bonds generated for 'chain 'B' and resid 221 through 224' Processing helix chain 'B' and resid 234 through 253 Processing helix chain 'B' and resid 266 through 272 Processing helix chain 'B' and resid 300 through 308 Processing helix chain 'B' and resid 361 through 382 Processing helix chain 'B' and resid 393 through 396 No H-bonds generated for 'chain 'B' and resid 393 through 396' Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'B' and resid 479 through 485 removed outlier: 3.813A pdb=" N SER B 483 " --> pdb=" O PRO B 479 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 256 through 258 removed outlier: 4.100A pdb=" N SER A 325 " --> pdb=" O MET A 258 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER A 326 " --> pdb=" O LYS A 350 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 350 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N CYS A 455 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N MET A 353 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N THR A 453 " --> pdb=" O MET A 353 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N GLY A 355 " --> pdb=" O ASN A 451 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ASN A 451 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR A 357 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR A 449 " --> pdb=" O THR A 357 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 449 " --> pdb=" O CYS A 425 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN A 451 " --> pdb=" O SER A 423 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR A 453 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N SER A 421 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYS A 455 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 10.080A pdb=" N VAL A 419 " --> pdb=" O CYS A 455 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 417 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 406 " --> pdb=" O VAL A 419 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 421 " --> pdb=" O PHE A 404 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE A 404 " --> pdb=" O SER A 421 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER A 423 " --> pdb=" O ARG A 402 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ARG A 402 " --> pdb=" O SER A 423 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 263 through 265 Processing sheet with id= C, first strand: chain 'B' and resid 256 through 258 removed outlier: 4.165A pdb=" N SER B 325 " --> pdb=" O MET B 258 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER B 326 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 350 " --> pdb=" O SER B 326 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS B 455 " --> pdb=" O VAL B 351 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET B 353 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N THR B 453 " --> pdb=" O MET B 353 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLY B 355 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASN B 451 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N SER B 421 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N CYS B 455 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N VAL B 419 " --> pdb=" O CYS B 455 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 406 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER B 421 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE B 404 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASP B 390 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N VAL B 188 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 263 through 265 Processing sheet with id= E, first strand: chain 'B' and resid 312 through 314 removed outlier: 7.656A pdb=" N MET B 436 " --> pdb=" O VAL B 313 " (cutoff:3.500A) 229 hydrogen bonds defined for protein. 579 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1888 1.33 - 1.45: 1429 1.45 - 1.57: 3629 1.57 - 1.69: 82 1.69 - 1.81: 56 Bond restraints: 7084 Sorted by residual: bond pdb=" C6 SSA B 601 " pdb=" N6 SSA B 601 " ideal model delta sigma weight residual 1.333 1.520 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" C6 SSA A 601 " pdb=" N6 SSA A 601 " ideal model delta sigma weight residual 1.333 1.514 -0.181 2.00e-02 2.50e+03 8.18e+01 bond pdb=" O5' SSA B 601 " pdb=" S1 SSA B 601 " ideal model delta sigma weight residual 1.581 1.730 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" O2S SSA B 601 " pdb=" S1 SSA B 601 " ideal model delta sigma weight residual 1.435 1.583 -0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" O2S SSA A 601 " pdb=" S1 SSA A 601 " ideal model delta sigma weight residual 1.435 1.579 -0.144 2.00e-02 2.50e+03 5.17e+01 ... (remaining 7079 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.22: 403 106.22 - 113.18: 3865 113.18 - 120.13: 2644 120.13 - 127.09: 2709 127.09 - 134.04: 152 Bond angle restraints: 9773 Sorted by residual: angle pdb=" O1S SSA B 601 " pdb=" S1 SSA B 601 " pdb=" O2S SSA B 601 " ideal model delta sigma weight residual 121.34 102.37 18.97 3.00e+00 1.11e-01 4.00e+01 angle pdb=" O1S SSA A 601 " pdb=" S1 SSA A 601 " pdb=" O2S SSA A 601 " ideal model delta sigma weight residual 121.34 102.72 18.62 3.00e+00 1.11e-01 3.85e+01 angle pdb=" N1 SSA B 601 " pdb=" C6 SSA B 601 " pdb=" N6 SSA B 601 " ideal model delta sigma weight residual 119.38 108.60 10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" N1 SSA A 601 " pdb=" C6 SSA A 601 " pdb=" N6 SSA A 601 " ideal model delta sigma weight residual 119.38 108.72 10.66 3.00e+00 1.11e-01 1.26e+01 angle pdb=" N PHE B 386 " pdb=" CA PHE B 386 " pdb=" C PHE B 386 " ideal model delta sigma weight residual 109.24 114.98 -5.74 1.67e+00 3.59e-01 1.18e+01 ... (remaining 9768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.35: 4057 30.35 - 60.71: 191 60.71 - 91.06: 49 91.06 - 121.41: 1 121.41 - 151.76: 2 Dihedral angle restraints: 4300 sinusoidal: 2117 harmonic: 2183 Sorted by residual: dihedral pdb=" O4' U C 9 " pdb=" C1' U C 9 " pdb=" N1 U C 9 " pdb=" C2 U C 9 " ideal model delta sinusoidal sigma weight residual -160.00 -8.24 -151.76 1 1.50e+01 4.44e-03 8.03e+01 dihedral pdb=" O4' C C 8 " pdb=" C1' C C 8 " pdb=" N1 C C 8 " pdb=" C2 C C 8 " ideal model delta sinusoidal sigma weight residual -160.00 -10.36 -149.64 1 1.50e+01 4.44e-03 7.95e+01 dihedral pdb=" O4' A C 45 " pdb=" C1' A C 45 " pdb=" N9 A C 45 " pdb=" C4 A C 45 " ideal model delta sinusoidal sigma weight residual -106.00 -173.42 67.42 1 1.70e+01 3.46e-03 2.05e+01 ... (remaining 4297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1076 0.118 - 0.235: 31 0.235 - 0.353: 0 0.353 - 0.470: 0 0.470 - 0.588: 2 Chirality restraints: 1109 Sorted by residual: chirality pdb=" CA SSA B 601 " pdb=" CB SSA B 601 " pdb=" C9 SSA B 601 " pdb=" N10 SSA B 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.06 0.59 2.00e-01 2.50e+01 8.64e+00 chirality pdb=" CA SSA A 601 " pdb=" CB SSA A 601 " pdb=" C9 SSA A 601 " pdb=" N10 SSA A 601 " both_signs ideal model delta sigma weight residual False -2.47 -3.03 0.57 2.00e-01 2.50e+01 8.01e+00 chirality pdb=" CA ARG A 227 " pdb=" N ARG A 227 " pdb=" C ARG A 227 " pdb=" CB ARG A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.33e-01 ... (remaining 1106 not shown) Planarity restraints: 1139 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 221 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.49e+00 pdb=" C SER B 221 " 0.041 2.00e-02 2.50e+03 pdb=" O SER B 221 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 222 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 45 " -0.028 2.00e-02 2.50e+03 1.33e-02 4.87e+00 pdb=" N9 A C 45 " 0.032 2.00e-02 2.50e+03 pdb=" C8 A C 45 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A C 45 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A C 45 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A C 45 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A C 45 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A C 45 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A C 45 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A C 45 " 0.006 2.00e-02 2.50e+03 pdb=" C4 A C 45 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 347 " -0.014 2.00e-02 2.50e+03 1.50e-02 3.37e+00 pdb=" CG HIS B 347 " 0.032 2.00e-02 2.50e+03 pdb=" ND1 HIS B 347 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 HIS B 347 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 HIS B 347 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS B 347 " -0.003 2.00e-02 2.50e+03 ... (remaining 1136 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.51: 51 2.51 - 3.11: 5284 3.11 - 3.71: 10927 3.71 - 4.30: 14981 4.30 - 4.90: 24199 Nonbonded interactions: 55442 Sorted by model distance: nonbonded pdb=" OH TYR A 329 " pdb=" OH TYR B 329 " model vdw 1.918 2.440 nonbonded pdb=" OG SSA A 601 " pdb=" O9 SSA A 601 " model vdw 2.005 2.440 nonbonded pdb=" OD1 ASN B 451 " pdb=" OG SSA B 601 " model vdw 2.019 2.440 nonbonded pdb=" OG SER A 224 " pdb=" OG SER A 228 " model vdw 2.020 2.440 nonbonded pdb=" O2' A C 45 " pdb=" O5' A C 46 " model vdw 2.039 2.440 ... (remaining 55437 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: 0.440 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: 1.480 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 24.660 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 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 : 0.010 0.187 7084 Z= 0.688 Angle : 1.045 18.967 9773 Z= 0.569 Chirality : 0.055 0.588 1109 Planarity : 0.004 0.045 1139 Dihedral : 17.756 151.765 2896 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.31 % Allowed : 12.66 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.29), residues: 751 helix: 2.82 (0.29), residues: 296 sheet: 1.13 (0.54), residues: 87 loop : 0.23 (0.29), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 409 HIS 0.016 0.002 HIS B 347 PHE 0.019 0.002 PHE B 404 TYR 0.019 0.003 TYR B 230 ARG 0.006 0.001 ARG A 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 262 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8645 (mtt) cc_final: 0.8163 (ttm) REVERT: A 218 LYS cc_start: 0.4545 (mtmt) cc_final: 0.4302 (pttt) REVERT: A 226 HIS cc_start: 0.7146 (t70) cc_final: 0.6778 (t-90) REVERT: A 244 ASN cc_start: 0.8206 (m-40) cc_final: 0.7830 (t0) REVERT: A 248 ASN cc_start: 0.7613 (m-40) cc_final: 0.7394 (t0) REVERT: A 343 TYR cc_start: 0.6439 (t80) cc_final: 0.6216 (t80) REVERT: A 369 GLU cc_start: 0.8398 (tp30) cc_final: 0.8165 (mm-30) REVERT: A 370 GLU cc_start: 0.8711 (tt0) cc_final: 0.8411 (tm-30) REVERT: A 378 ILE cc_start: 0.7865 (mt) cc_final: 0.7592 (mm) REVERT: A 385 HIS cc_start: 0.5666 (t70) cc_final: 0.5208 (t70) REVERT: A 464 LEU cc_start: 0.7543 (mt) cc_final: 0.7160 (mt) REVERT: A 474 SER cc_start: 0.7368 (m) cc_final: 0.6596 (p) REVERT: B 99 LEU cc_start: 0.6943 (mt) cc_final: 0.6582 (mt) REVERT: B 290 ARG cc_start: 0.8667 (tpt90) cc_final: 0.8258 (mmm-85) REVERT: B 344 ARG cc_start: 0.6462 (mmt180) cc_final: 0.6168 (mmm-85) REVERT: B 363 GLN cc_start: 0.7819 (mp10) cc_final: 0.7457 (tt0) REVERT: B 435 ILE cc_start: 0.6856 (mt) cc_final: 0.6194 (mt) REVERT: B 501 ILE cc_start: 0.8156 (mm) cc_final: 0.7781 (mt) outliers start: 2 outliers final: 0 residues processed: 264 average time/residue: 0.2194 time to fit residues: 73.6730 Evaluate side-chains 138 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 0.0000 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.9790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 375 GLN A 499 GLN B 57 GLN B 102 GLN ** B 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 7084 Z= 0.302 Angle : 0.679 9.108 9773 Z= 0.348 Chirality : 0.041 0.200 1109 Planarity : 0.006 0.081 1139 Dihedral : 16.876 153.981 1434 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.56 (0.30), residues: 751 helix: 1.94 (0.30), residues: 274 sheet: 1.39 (0.55), residues: 87 loop : 0.38 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 409 HIS 0.008 0.001 HIS B 205 PHE 0.023 0.002 PHE B 163 TYR 0.027 0.003 TYR B 329 ARG 0.005 0.001 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8393 (mtt) cc_final: 0.8056 (ttm) REVERT: A 218 LYS cc_start: 0.4615 (mtmt) cc_final: 0.4216 (pttt) REVERT: A 244 ASN cc_start: 0.8265 (m-40) cc_final: 0.7804 (t0) REVERT: A 378 ILE cc_start: 0.7807 (mt) cc_final: 0.7584 (mm) REVERT: A 426 THR cc_start: 0.7331 (p) cc_final: 0.6715 (p) REVERT: B 78 LYS cc_start: 0.7516 (tptt) cc_final: 0.6779 (mmtp) REVERT: B 210 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8452 (tt0) REVERT: B 250 LEU cc_start: 0.8812 (mm) cc_final: 0.8399 (mm) REVERT: B 340 ARG cc_start: 0.6636 (mmp-170) cc_final: 0.6156 (mtm180) REVERT: B 344 ARG cc_start: 0.6830 (mmt180) cc_final: 0.6581 (mmm160) REVERT: B 353 MET cc_start: 0.6614 (mtm) cc_final: 0.5943 (mtm) REVERT: B 487 THR cc_start: 0.8026 (m) cc_final: 0.7808 (p) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2224 time to fit residues: 51.3439 Evaluate side-chains 131 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 48 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 0.0570 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 56 optimal weight: 0.0770 chunk 53 optimal weight: 3.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 451 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6201 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7084 Z= 0.217 Angle : 0.605 7.587 9773 Z= 0.307 Chirality : 0.040 0.205 1109 Planarity : 0.005 0.044 1139 Dihedral : 16.659 153.508 1434 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.16 % Allowed : 2.19 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 1.15 (0.30), residues: 751 helix: 1.60 (0.31), residues: 268 sheet: 0.64 (0.47), residues: 103 loop : 0.31 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 409 HIS 0.013 0.001 HIS A 226 PHE 0.031 0.002 PHE B 63 TYR 0.013 0.002 TYR B 329 ARG 0.004 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8404 (mtt) cc_final: 0.8088 (ttm) REVERT: A 218 LYS cc_start: 0.4690 (mtmt) cc_final: 0.4224 (pttt) REVERT: A 244 ASN cc_start: 0.8107 (m-40) cc_final: 0.7732 (t0) REVERT: A 258 MET cc_start: 0.6716 (mtp) cc_final: 0.6488 (mmm) REVERT: A 327 THR cc_start: 0.7172 (p) cc_final: 0.6849 (p) REVERT: A 332 GLU cc_start: 0.6140 (pm20) cc_final: 0.5640 (pm20) REVERT: B 78 LYS cc_start: 0.7647 (tptt) cc_final: 0.6964 (mmtp) REVERT: B 185 GLN cc_start: 0.7539 (mm110) cc_final: 0.7049 (mp10) REVERT: B 224 SER cc_start: 0.9112 (p) cc_final: 0.8679 (p) REVERT: B 250 LEU cc_start: 0.8500 (mm) cc_final: 0.8171 (mm) REVERT: B 290 ARG cc_start: 0.8688 (tpt90) cc_final: 0.8462 (mmm-85) REVERT: B 340 ARG cc_start: 0.6720 (mmp-170) cc_final: 0.6252 (ttm170) REVERT: B 344 ARG cc_start: 0.6962 (mmt180) cc_final: 0.6710 (mmm160) REVERT: B 353 MET cc_start: 0.6685 (mtm) cc_final: 0.6210 (mtm) REVERT: B 407 GLU cc_start: 0.8258 (tt0) cc_final: 0.7945 (tt0) REVERT: B 464 LEU cc_start: 0.6853 (mt) cc_final: 0.6579 (mt) outliers start: 1 outliers final: 0 residues processed: 159 average time/residue: 0.2082 time to fit residues: 43.3728 Evaluate side-chains 123 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.0170 chunk 7 optimal weight: 0.0270 chunk 33 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 overall best weight: 2.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7084 Z= 0.260 Angle : 0.615 6.346 9773 Z= 0.312 Chirality : 0.040 0.195 1109 Planarity : 0.005 0.090 1139 Dihedral : 16.679 154.959 1434 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.84 (0.30), residues: 751 helix: 1.39 (0.32), residues: 265 sheet: 0.66 (0.47), residues: 94 loop : 0.05 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 409 HIS 0.007 0.001 HIS B 347 PHE 0.012 0.002 PHE A 371 TYR 0.016 0.002 TYR B 45 ARG 0.005 0.001 ARG A 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8434 (mtt) cc_final: 0.8081 (ttm) REVERT: A 244 ASN cc_start: 0.8218 (m-40) cc_final: 0.7700 (t0) REVERT: A 274 MET cc_start: 0.3681 (mtp) cc_final: 0.3359 (mtt) REVERT: A 301 GLU cc_start: 0.8041 (tp30) cc_final: 0.7800 (tp30) REVERT: A 410 MET cc_start: 0.4972 (mtt) cc_final: 0.4541 (mtt) REVERT: B 58 LEU cc_start: 0.7225 (mt) cc_final: 0.6954 (mp) REVERT: B 78 LYS cc_start: 0.7952 (tptt) cc_final: 0.7243 (mmtp) REVERT: B 185 GLN cc_start: 0.7474 (mm110) cc_final: 0.7148 (mp10) REVERT: B 224 SER cc_start: 0.9100 (p) cc_final: 0.8700 (p) REVERT: B 274 MET cc_start: 0.7209 (mtt) cc_final: 0.6934 (mtm) REVERT: B 291 PHE cc_start: 0.7749 (m-80) cc_final: 0.7538 (m-80) REVERT: B 340 ARG cc_start: 0.6853 (mmp-170) cc_final: 0.6308 (mtm180) REVERT: B 344 ARG cc_start: 0.7052 (mmt180) cc_final: 0.6788 (mmm160) REVERT: B 353 MET cc_start: 0.6754 (mtm) cc_final: 0.6522 (mtm) REVERT: B 363 GLN cc_start: 0.7655 (mp10) cc_final: 0.7147 (tt0) REVERT: B 407 GLU cc_start: 0.8300 (tt0) cc_final: 0.8010 (tt0) REVERT: B 464 LEU cc_start: 0.7063 (mt) cc_final: 0.6832 (mt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.2219 time to fit residues: 43.9929 Evaluate side-chains 116 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 19 optimal weight: 0.0980 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7084 Z= 0.177 Angle : 0.564 6.975 9773 Z= 0.286 Chirality : 0.040 0.219 1109 Planarity : 0.004 0.038 1139 Dihedral : 16.536 153.964 1434 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.73 (0.29), residues: 751 helix: 1.27 (0.32), residues: 267 sheet: 0.65 (0.46), residues: 96 loop : -0.03 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 409 HIS 0.005 0.001 HIS B 347 PHE 0.024 0.001 PHE B 63 TYR 0.025 0.002 TYR A 230 ARG 0.008 0.001 ARG B 431 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8398 (mtt) cc_final: 0.8097 (ttm) REVERT: A 244 ASN cc_start: 0.8106 (m-40) cc_final: 0.7695 (t0) REVERT: A 258 MET cc_start: 0.7571 (mmt) cc_final: 0.7326 (mmm) REVERT: A 274 MET cc_start: 0.3446 (mtp) cc_final: 0.3193 (mtt) REVERT: A 356 VAL cc_start: 0.9020 (t) cc_final: 0.8707 (t) REVERT: A 410 MET cc_start: 0.4765 (mtt) cc_final: 0.4391 (mtt) REVERT: B 78 LYS cc_start: 0.7972 (tptt) cc_final: 0.7229 (mmtp) REVERT: B 185 GLN cc_start: 0.7456 (mm110) cc_final: 0.7118 (mp10) REVERT: B 224 SER cc_start: 0.9110 (p) cc_final: 0.8663 (p) REVERT: B 274 MET cc_start: 0.7250 (mtt) cc_final: 0.6944 (mtm) REVERT: B 340 ARG cc_start: 0.6890 (mmp-170) cc_final: 0.6330 (mtm180) REVERT: B 343 TYR cc_start: 0.6785 (t80) cc_final: 0.6569 (t80) REVERT: B 344 ARG cc_start: 0.7017 (mmt180) cc_final: 0.6778 (mmm160) REVERT: B 353 MET cc_start: 0.6745 (mtm) cc_final: 0.6342 (mtm) REVERT: B 363 GLN cc_start: 0.7549 (mp10) cc_final: 0.7027 (tt0) REVERT: B 407 GLU cc_start: 0.8237 (tt0) cc_final: 0.7869 (tt0) REVERT: B 464 LEU cc_start: 0.7002 (mt) cc_final: 0.6801 (mt) REVERT: B 500 TYR cc_start: 0.8296 (t80) cc_final: 0.8087 (t80) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2190 time to fit residues: 45.5457 Evaluate side-chains 117 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 75 optimal weight: 0.0470 chunk 62 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.0970 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 20.0000 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 363 GLN B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.5521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7084 Z= 0.167 Angle : 0.552 6.449 9773 Z= 0.280 Chirality : 0.039 0.206 1109 Planarity : 0.004 0.031 1139 Dihedral : 16.393 152.709 1434 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 (0.30), residues: 751 helix: 1.26 (0.33), residues: 270 sheet: 0.80 (0.48), residues: 100 loop : 0.04 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 93 HIS 0.007 0.001 HIS B 347 PHE 0.022 0.001 PHE B 354 TYR 0.041 0.002 TYR A 230 ARG 0.005 0.001 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8402 (mtt) cc_final: 0.8095 (ttm) REVERT: A 230 TYR cc_start: 0.8218 (m-10) cc_final: 0.7859 (m-10) REVERT: A 244 ASN cc_start: 0.8053 (m-40) cc_final: 0.7593 (t0) REVERT: A 258 MET cc_start: 0.7366 (mmt) cc_final: 0.7054 (mmm) REVERT: A 390 ASP cc_start: 0.6756 (t0) cc_final: 0.6472 (t0) REVERT: A 410 MET cc_start: 0.4762 (mtt) cc_final: 0.3810 (mtm) REVERT: A 484 TYR cc_start: 0.6422 (m-80) cc_final: 0.6201 (m-80) REVERT: B 59 ASP cc_start: 0.5778 (t0) cc_final: 0.5363 (t0) REVERT: B 185 GLN cc_start: 0.7458 (mm110) cc_final: 0.7225 (mp10) REVERT: B 224 SER cc_start: 0.9138 (p) cc_final: 0.8689 (p) REVERT: B 250 LEU cc_start: 0.8245 (mm) cc_final: 0.8036 (mm) REVERT: B 274 MET cc_start: 0.7339 (mtt) cc_final: 0.6801 (mtm) REVERT: B 340 ARG cc_start: 0.6892 (mmp-170) cc_final: 0.6342 (mtm180) REVERT: B 344 ARG cc_start: 0.7002 (mmt180) cc_final: 0.6753 (mmm160) REVERT: B 353 MET cc_start: 0.6690 (mtm) cc_final: 0.6411 (mtm) REVERT: B 363 GLN cc_start: 0.7571 (mp10) cc_final: 0.7105 (tt0) REVERT: B 407 GLU cc_start: 0.8194 (tt0) cc_final: 0.7924 (tt0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.2178 time to fit residues: 40.9985 Evaluate side-chains 116 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 47 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.0870 chunk 22 optimal weight: 6.9990 overall best weight: 0.8762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS A 363 GLN B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.5755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7084 Z= 0.191 Angle : 0.562 6.533 9773 Z= 0.285 Chirality : 0.039 0.211 1109 Planarity : 0.005 0.049 1139 Dihedral : 16.374 152.403 1434 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.30), residues: 751 helix: 1.25 (0.33), residues: 267 sheet: 0.80 (0.48), residues: 100 loop : -0.05 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 93 HIS 0.007 0.001 HIS B 347 PHE 0.020 0.002 PHE B 63 TYR 0.029 0.001 TYR A 230 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8390 (mtt) cc_final: 0.8089 (ttm) REVERT: A 230 TYR cc_start: 0.8293 (m-80) cc_final: 0.8019 (m-10) REVERT: A 244 ASN cc_start: 0.8063 (m-40) cc_final: 0.7594 (t0) REVERT: A 258 MET cc_start: 0.7457 (mmt) cc_final: 0.7086 (mmm) REVERT: A 376 MET cc_start: 0.7869 (mtp) cc_final: 0.7514 (mtp) REVERT: A 390 ASP cc_start: 0.6691 (t0) cc_final: 0.6419 (t0) REVERT: A 410 MET cc_start: 0.4763 (mtt) cc_final: 0.4357 (mtt) REVERT: B 187 ARG cc_start: 0.6425 (tpt90) cc_final: 0.6203 (tpt170) REVERT: B 224 SER cc_start: 0.9120 (p) cc_final: 0.8661 (p) REVERT: B 250 LEU cc_start: 0.8228 (mm) cc_final: 0.8013 (mm) REVERT: B 274 MET cc_start: 0.7319 (mtt) cc_final: 0.6918 (mtm) REVERT: B 287 ASP cc_start: 0.8011 (t0) cc_final: 0.7782 (t0) REVERT: B 340 ARG cc_start: 0.6956 (mmp-170) cc_final: 0.6427 (mtm180) REVERT: B 343 TYR cc_start: 0.6690 (t80) cc_final: 0.6457 (t80) REVERT: B 344 ARG cc_start: 0.6997 (mmt180) cc_final: 0.6774 (mmm160) REVERT: B 353 MET cc_start: 0.6715 (mtm) cc_final: 0.6344 (mtm) REVERT: B 407 GLU cc_start: 0.8255 (tt0) cc_final: 0.7968 (tt0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1818 time to fit residues: 37.1601 Evaluate side-chains 115 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.5980 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 226 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN A 468 ASN A 495 HIS B 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.6538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 7084 Z= 0.355 Angle : 0.712 11.321 9773 Z= 0.365 Chirality : 0.044 0.209 1109 Planarity : 0.006 0.047 1139 Dihedral : 16.878 154.737 1434 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.09 (0.30), residues: 751 helix: 0.78 (0.32), residues: 259 sheet: 0.43 (0.51), residues: 97 loop : -0.47 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 409 HIS 0.010 0.002 HIS B 347 PHE 0.019 0.003 PHE B 354 TYR 0.028 0.003 TYR B 47 ARG 0.005 0.001 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.743 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8352 (mtt) cc_final: 0.7962 (ttm) REVERT: A 211 LYS cc_start: 0.8200 (mtmt) cc_final: 0.7953 (tptt) REVERT: A 244 ASN cc_start: 0.8224 (m-40) cc_final: 0.7706 (t0) REVERT: A 258 MET cc_start: 0.7462 (mmt) cc_final: 0.7089 (mmt) REVERT: A 385 HIS cc_start: 0.5083 (t70) cc_final: 0.4844 (t70) REVERT: A 390 ASP cc_start: 0.6747 (t0) cc_final: 0.6387 (t0) REVERT: B 210 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7766 (mm-30) REVERT: B 224 SER cc_start: 0.9122 (p) cc_final: 0.8716 (p) REVERT: B 344 ARG cc_start: 0.7287 (mmt180) cc_final: 0.6903 (mmm160) REVERT: B 353 MET cc_start: 0.7016 (mtm) cc_final: 0.6706 (mtm) REVERT: B 381 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7643 (tt0) REVERT: B 428 PHE cc_start: 0.7667 (t80) cc_final: 0.7373 (t80) REVERT: B 436 MET cc_start: 0.7651 (mpp) cc_final: 0.7375 (mmt) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.1900 time to fit residues: 32.4261 Evaluate side-chains 103 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 0.0770 chunk 51 optimal weight: 0.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN A 226 HIS B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6415 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 7084 Z= 0.203 Angle : 0.622 7.775 9773 Z= 0.314 Chirality : 0.040 0.168 1109 Planarity : 0.005 0.045 1139 Dihedral : 16.669 152.692 1434 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.30), residues: 751 helix: 1.03 (0.33), residues: 259 sheet: 0.04 (0.45), residues: 108 loop : -0.33 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 409 HIS 0.006 0.001 HIS B 347 PHE 0.020 0.002 PHE B 354 TYR 0.018 0.002 TYR B 45 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8403 (mtt) cc_final: 0.7926 (ttm) REVERT: A 216 ARG cc_start: 0.6649 (ttt180) cc_final: 0.6266 (ptt90) REVERT: A 218 LYS cc_start: 0.4864 (mtmt) cc_final: 0.4370 (mtmt) REVERT: A 244 ASN cc_start: 0.8073 (m-40) cc_final: 0.7622 (t0) REVERT: A 258 MET cc_start: 0.7402 (mmt) cc_final: 0.7085 (mmm) REVERT: A 301 GLU cc_start: 0.7881 (tp30) cc_final: 0.7517 (tp30) REVERT: A 367 LEU cc_start: 0.9229 (tp) cc_final: 0.8958 (tp) REVERT: A 390 ASP cc_start: 0.7191 (t0) cc_final: 0.6728 (t0) REVERT: A 392 PRO cc_start: 0.7883 (Cg_endo) cc_final: 0.7645 (Cg_exo) REVERT: B 69 GLU cc_start: 0.7572 (tp30) cc_final: 0.7128 (tt0) REVERT: B 75 GLU cc_start: 0.6624 (tp30) cc_final: 0.6134 (mm-30) REVERT: B 187 ARG cc_start: 0.6357 (tpt170) cc_final: 0.6142 (tpt170) REVERT: B 224 SER cc_start: 0.9144 (p) cc_final: 0.8645 (p) REVERT: B 344 ARG cc_start: 0.7123 (mmt180) cc_final: 0.6721 (mmm160) REVERT: B 381 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7615 (tt0) REVERT: B 407 GLU cc_start: 0.8085 (tt0) cc_final: 0.7502 (tt0) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1952 time to fit residues: 35.5686 Evaluate side-chains 107 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.2980 chunk 71 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 57 optimal weight: 0.0060 chunk 9 optimal weight: 3.9990 overall best weight: 0.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS B 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 7084 Z= 0.196 Angle : 0.606 6.970 9773 Z= 0.303 Chirality : 0.039 0.160 1109 Planarity : 0.005 0.045 1139 Dihedral : 16.558 150.642 1434 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.19 (0.30), residues: 751 helix: 0.96 (0.33), residues: 261 sheet: 0.13 (0.48), residues: 100 loop : -0.38 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 409 HIS 0.007 0.001 HIS B 347 PHE 0.019 0.002 PHE B 354 TYR 0.030 0.002 TYR A 230 ARG 0.004 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8388 (mtt) cc_final: 0.7910 (ttm) REVERT: A 218 LYS cc_start: 0.4995 (mtmt) cc_final: 0.4634 (pttt) REVERT: A 244 ASN cc_start: 0.8082 (m-40) cc_final: 0.7565 (t0) REVERT: A 258 MET cc_start: 0.7389 (mmt) cc_final: 0.7046 (mmt) REVERT: A 301 GLU cc_start: 0.8005 (tp30) cc_final: 0.7651 (tp30) REVERT: A 367 LEU cc_start: 0.9260 (tp) cc_final: 0.8986 (tp) REVERT: A 392 PRO cc_start: 0.7820 (Cg_endo) cc_final: 0.7534 (Cg_exo) REVERT: B 69 GLU cc_start: 0.7641 (tp30) cc_final: 0.7244 (tt0) REVERT: B 187 ARG cc_start: 0.6290 (tpt170) cc_final: 0.5997 (tpt170) REVERT: B 224 SER cc_start: 0.9114 (p) cc_final: 0.8673 (p) REVERT: B 287 ASP cc_start: 0.7878 (t0) cc_final: 0.7608 (t0) REVERT: B 344 ARG cc_start: 0.7071 (mmt180) cc_final: 0.6702 (mmm160) REVERT: B 381 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7549 (tt0) REVERT: B 407 GLU cc_start: 0.7969 (tt0) cc_final: 0.7528 (tt0) REVERT: B 428 PHE cc_start: 0.7433 (t80) cc_final: 0.7108 (t80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2085 time to fit residues: 37.3943 Evaluate side-chains 102 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 HIS A 226 HIS ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.175470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.147180 restraints weight = 9620.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.150714 restraints weight = 5983.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.153185 restraints weight = 4211.020| |-----------------------------------------------------------------------------| r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.7148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7084 Z= 0.261 Angle : 0.625 6.633 9773 Z= 0.317 Chirality : 0.041 0.175 1109 Planarity : 0.005 0.044 1139 Dihedral : 16.659 150.527 1434 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.08 (0.30), residues: 751 helix: 0.91 (0.33), residues: 261 sheet: 0.11 (0.50), residues: 100 loop : -0.50 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 409 HIS 0.007 0.001 HIS B 347 PHE 0.020 0.002 PHE A 386 TYR 0.030 0.002 TYR A 230 ARG 0.005 0.001 ARG A 216 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1771.05 seconds wall clock time: 33 minutes 3.22 seconds (1983.22 seconds total)