Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 10:41:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/04_2023/7u2a_26310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/04_2023/7u2a_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_26310/04_2023/7u2a_26310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/04_2023/7u2a_26310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/04_2023/7u2a_26310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/04_2023/7u2a_26310_updated.pdb" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 9 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: 4.58, per 1000 atoms: 0.67 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: 3.39 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: 2.67 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: 2.10 Time building geometry restraints manager: 3.55 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: 4003 30.35 - 60.71: 145 60.71 - 91.06: 7 91.06 - 121.41: 1 121.41 - 151.76: 2 Dihedral angle restraints: 4158 sinusoidal: 1975 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 4155 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: 0.240 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: 1.760 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.330 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.660 ------------------------------------------------------------------------------- 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 : 14.762 151.765 2754 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 % 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 *********************** 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 : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 264 average time/residue: 0.2261 time to fit residues: 75.3905 Evaluate side-chains 134 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.764 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0294 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.6165 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.140 7084 Z= 0.302 Angle : 0.698 9.178 9773 Z= 0.355 Chirality : 0.042 0.223 1109 Planarity : 0.006 0.068 1139 Dihedral : 10.548 153.729 1292 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer Outliers : 0.31 % 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: 1.42 (0.29), residues: 751 helix: 1.74 (0.30), residues: 274 sheet: 1.30 (0.55), residues: 87 loop : 0.38 (0.30), residues: 390 *********************** 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 181 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 179 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.2098 time to fit residues: 49.2175 Evaluate side-chains 128 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0809 ------------------------------------------------------------------------------- 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: 5.9990 chunk 21 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6264 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 7084 Z= 0.241 Angle : 0.630 7.293 9773 Z= 0.320 Chirality : 0.041 0.203 1109 Planarity : 0.005 0.068 1139 Dihedral : 10.418 153.970 1292 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.13 % Favored : 97.74 % Rotamer Outliers : 0.31 % 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: 0.95 (0.29), residues: 751 helix: 1.33 (0.32), residues: 261 sheet: 0.85 (0.48), residues: 93 loop : 0.20 (0.30), residues: 397 *********************** 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 161 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 0.753 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 161 average time/residue: 0.2277 time to fit residues: 46.9550 Evaluate side-chains 112 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0025 ------------------------------------------------------------------------------- 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: 0.2980 chunk 7 optimal weight: 0.0070 chunk 33 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 0.2980 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 42 optimal weight: 20.0000 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 7084 Z= 0.164 Angle : 0.567 6.379 9773 Z= 0.287 Chirality : 0.039 0.217 1109 Planarity : 0.004 0.042 1139 Dihedral : 10.374 153.045 1292 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.00 % 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: 1.24 (0.32), residues: 273 sheet: 0.83 (0.48), residues: 98 loop : 0.08 (0.31), residues: 380 *********************** 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 157 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.715 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2149 time to fit residues: 44.2777 Evaluate side-chains 112 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.866 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0379 ------------------------------------------------------------------------------- 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: 0.6980 chunk 31 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 10.9990 chunk 38 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 overall best weight: 3.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN A 448 HIS A 468 ASN A 495 HIS B 469 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 7084 Z= 0.400 Angle : 0.756 8.032 9773 Z= 0.389 Chirality : 0.046 0.219 1109 Planarity : 0.006 0.049 1139 Dihedral : 11.185 158.878 1292 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.00 % 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: -0.12 (0.29), residues: 751 helix: 0.61 (0.31), residues: 266 sheet: 0.18 (0.48), residues: 102 loop : -0.59 (0.29), residues: 383 *********************** 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 142 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2157 time to fit residues: 39.9419 Evaluate side-chains 99 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.744 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0364 ------------------------------------------------------------------------------- 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: 10.0000 chunk 18 optimal weight: 0.3980 chunk 75 optimal weight: 0.0470 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.6549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 7084 Z= 0.182 Angle : 0.619 7.296 9773 Z= 0.314 Chirality : 0.040 0.185 1109 Planarity : 0.005 0.062 1139 Dihedral : 10.929 156.890 1292 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.00 % 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: 0.10 (0.29), residues: 751 helix: 0.78 (0.32), residues: 265 sheet: -0.02 (0.47), residues: 106 loop : -0.34 (0.30), residues: 380 *********************** 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 139 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2135 time to fit residues: 38.8236 Evaluate side-chains 100 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1464 ------------------------------------------------------------------------------- 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: 0.8980 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 47 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6454 moved from start: 0.6794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 7084 Z= 0.214 Angle : 0.603 6.717 9773 Z= 0.305 Chirality : 0.040 0.163 1109 Planarity : 0.005 0.045 1139 Dihedral : 10.775 154.936 1292 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer Outliers : 0.00 % 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: 0.01 (0.30), residues: 751 helix: 0.81 (0.32), residues: 271 sheet: -0.13 (0.49), residues: 102 loop : -0.48 (0.30), residues: 378 *********************** 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 127 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1565 time to fit residues: 28.1918 Evaluate side-chains 102 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0162 ------------------------------------------------------------------------------- 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: 0.8980 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** 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: 0.6443 moved from start: 0.7008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 7084 Z= 0.202 Angle : 0.600 6.367 9773 Z= 0.301 Chirality : 0.040 0.160 1109 Planarity : 0.005 0.043 1139 Dihedral : 10.725 153.641 1292 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.00 % 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: -0.02 (0.30), residues: 751 helix: 0.80 (0.32), residues: 270 sheet: -0.07 (0.52), residues: 98 loop : -0.52 (0.30), residues: 383 *********************** 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 121 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1549 time to fit residues: 26.4858 Evaluate side-chains 97 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.702 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9421 ------------------------------------------------------------------------------- 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: 0.8980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** 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: 0.6479 moved from start: 0.7236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 7084 Z= 0.225 Angle : 0.600 6.681 9773 Z= 0.303 Chirality : 0.040 0.161 1109 Planarity : 0.005 0.045 1139 Dihedral : 10.766 152.441 1292 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.00 % 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: -0.07 (0.30), residues: 751 helix: 0.82 (0.33), residues: 272 sheet: -0.18 (0.50), residues: 106 loop : -0.60 (0.30), residues: 373 *********************** 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 119 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1792 time to fit residues: 29.3330 Evaluate side-chains 97 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 0.768 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0357 ------------------------------------------------------------------------------- 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: 0.0070 chunk 71 optimal weight: 5.9990 chunk 61 optimal weight: 0.0170 chunk 6 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 49 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** 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: 0.6438 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7084 Z= 0.171 Angle : 0.578 6.414 9773 Z= 0.293 Chirality : 0.039 0.158 1109 Planarity : 0.005 0.044 1139 Dihedral : 10.702 150.560 1292 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.00 % 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: -0.03 (0.30), residues: 751 helix: 0.78 (0.33), residues: 272 sheet: -0.36 (0.49), residues: 110 loop : -0.42 (0.30), residues: 369 ********************** 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 115 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.1709 time to fit residues: 27.4396 Evaluate side-chains 93 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.783 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0810 ------------------------------------------------------------------------------- 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: 4.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 HIS A 363 GLN ** B 205 HIS ** 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 = 0.4213 r_free = 0.4213 target = 0.170543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.142281 restraints weight = 9690.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.145772 restraints weight = 5994.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148104 restraints weight = 4225.214| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.7595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 7084 Z= 0.294 Angle : 0.649 6.608 9773 Z= 0.330 Chirality : 0.041 0.166 1109 Planarity : 0.005 0.044 1139 Dihedral : 11.007 150.933 1292 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer Outliers : 0.00 % 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: -0.12 (0.30), residues: 751 helix: 0.73 (0.32), residues: 270 sheet: -0.44 (0.49), residues: 110 loop : -0.49 (0.31), residues: 371 =============================================================================== Job complete usr+sys time: 1564.25 seconds wall clock time: 29 minutes 11.55 seconds (1751.55 seconds total)