Starting phenix.real_space_refine on Fri Dec 8 03:42:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/12_2023/7u2a_26310_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/12_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_26310/12_2023/7u2a_26310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/12_2023/7u2a_26310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/12_2023/7u2a_26310_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u2a_26310/12_2023/7u2a_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 5.56, per 1000 atoms: 0.81 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: 3.22 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: 2.91 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: 1.95 Time building geometry restraints manager: 3.36 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: 0.980 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: 0.000 Extract box with map and model: 1.350 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 26.220 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- 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 : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 264 average time/residue: 0.2177 time to fit residues: 72.9914 Evaluate side-chains 134 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.790 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0204 ------------------------------------------------------------------------------- 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: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 7084 Z= 0.279 Angle : 0.694 9.126 9773 Z= 0.354 Chirality : 0.042 0.214 1109 Planarity : 0.006 0.060 1139 Dihedral : 16.861 154.079 1434 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.47 % Allowed : 4.84 % Favored : 94.69 % 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: 1.40 (0.29), residues: 751 helix: 1.72 (0.30), residues: 274 sheet: 1.31 (0.55), residues: 87 loop : 0.37 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 409 HIS 0.007 0.002 HIS B 205 PHE 0.022 0.002 PHE B 163 TYR 0.026 0.003 TYR B 329 ARG 0.004 0.001 ARG A 340 *********************** 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 183 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 180 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 183 average time/residue: 0.2035 time to fit residues: 48.5540 Evaluate side-chains 128 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 127 time to evaluate : 0.579 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0554 time to fit residues: 0.9103 ------------------------------------------------------------------------------- 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: 7.9990 chunk 21 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 HIS ** 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: 0.6378 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 7084 Z= 0.334 Angle : 0.700 7.817 9773 Z= 0.358 Chirality : 0.043 0.183 1109 Planarity : 0.005 0.046 1139 Dihedral : 16.845 156.860 1434 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.26 % Favored : 97.60 % Rotamer: Outliers : 0.31 % Allowed : 4.22 % Favored : 95.47 % 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: 0.66 (0.29), residues: 751 helix: 1.06 (0.31), residues: 260 sheet: 0.79 (0.49), residues: 92 loop : 0.04 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 409 HIS 0.010 0.002 HIS B 347 PHE 0.031 0.002 PHE B 63 TYR 0.021 0.003 TYR B 45 ARG 0.006 0.001 ARG A 340 *********************** 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 165 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 163 time to evaluate : 0.779 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 165 average time/residue: 0.2303 time to fit residues: 48.5883 Evaluate side-chains 102 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0626 time to fit residues: 1.0574 ------------------------------------------------------------------------------- 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: 4.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.5495 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= 0.221 Angle : 0.596 6.363 9773 Z= 0.304 Chirality : 0.040 0.192 1109 Planarity : 0.005 0.047 1139 Dihedral : 16.796 157.477 1434 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % 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: 0.53 (0.29), residues: 751 helix: 1.17 (0.32), residues: 265 sheet: 0.34 (0.45), residues: 106 loop : -0.15 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 409 HIS 0.006 0.001 HIS B 347 PHE 0.024 0.002 PHE B 428 TYR 0.024 0.002 TYR A 230 ARG 0.006 0.001 ARG A 340 *********************** 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 149 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.767 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2972 time to fit residues: 58.8999 Evaluate side-chains 101 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2564 ------------------------------------------------------------------------------- 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: 3.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 38 optimal weight: 0.0170 chunk 67 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7084 Z= 0.192 Angle : 0.581 7.036 9773 Z= 0.293 Chirality : 0.039 0.193 1109 Planarity : 0.005 0.044 1139 Dihedral : 16.649 156.223 1434 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % 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: 0.46 (0.30), residues: 751 helix: 1.10 (0.32), residues: 267 sheet: 0.12 (0.47), residues: 106 loop : -0.12 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 93 HIS 0.006 0.001 HIS B 347 PHE 0.020 0.002 PHE B 354 TYR 0.031 0.002 TYR A 230 ARG 0.006 0.001 ARG A 340 *********************** 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 141 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2227 time to fit residues: 41.4648 Evaluate side-chains 106 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0044 ------------------------------------------------------------------------------- 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: 1.9990 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.6191 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= 0.221 Angle : 0.596 6.652 9773 Z= 0.301 Chirality : 0.040 0.178 1109 Planarity : 0.005 0.055 1139 Dihedral : 16.629 156.023 1434 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % 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: 0.31 (0.30), residues: 751 helix: 1.07 (0.33), residues: 267 sheet: 0.17 (0.49), residues: 94 loop : -0.33 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 409 HIS 0.007 0.001 HIS B 347 PHE 0.015 0.002 PHE B 428 TYR 0.014 0.002 TYR B 45 ARG 0.007 0.001 ARG A 216 *********************** 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 144 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1767 time to fit residues: 34.4867 Evaluate side-chains 109 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9090 ------------------------------------------------------------------------------- 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: 1.9990 chunk 42 optimal weight: 20.0000 chunk 63 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.6551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7084 Z= 0.226 Angle : 0.600 6.497 9773 Z= 0.303 Chirality : 0.040 0.183 1109 Planarity : 0.005 0.045 1139 Dihedral : 16.639 155.528 1434 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 0.95 (0.33), residues: 267 sheet: -0.25 (0.46), residues: 106 loop : -0.38 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 93 HIS 0.007 0.001 HIS B 347 PHE 0.019 0.002 PHE A 247 TYR 0.033 0.002 TYR A 230 ARG 0.007 0.001 ARG A 340 *********************** 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 133 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.746 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1940 time to fit residues: 34.5325 Evaluate side-chains 98 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 0.706 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9559 ------------------------------------------------------------------------------- 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: 5.9990 chunk 47 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN A 468 ASN B 239 GLN B 311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.7198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 7084 Z= 0.378 Angle : 0.757 7.922 9773 Z= 0.385 Chirality : 0.045 0.256 1109 Planarity : 0.006 0.087 1139 Dihedral : 17.193 158.016 1434 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: -0.46 (0.29), residues: 751 helix: 0.53 (0.32), residues: 265 sheet: -0.48 (0.47), residues: 106 loop : -0.80 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 409 HIS 0.008 0.002 HIS B 347 PHE 0.021 0.003 PHE B 428 TYR 0.021 0.003 TYR B 47 ARG 0.006 0.001 ARG B 97 *********************** 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 122 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.1889 time to fit residues: 30.9435 Evaluate side-chains 88 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.719 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9832 ------------------------------------------------------------------------------- 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: 0.7980 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 69 optimal weight: 9.9990 chunk 46 optimal weight: 0.0040 chunk 74 optimal weight: 0.9990 chunk 45 optimal weight: 0.0370 chunk 35 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.3670 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN B 239 GLN B 495 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.7302 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= 0.177 Angle : 0.635 6.664 9773 Z= 0.320 Chirality : 0.041 0.175 1109 Planarity : 0.005 0.041 1139 Dihedral : 16.836 155.340 1434 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 (0.29), residues: 751 helix: 0.71 (0.32), residues: 260 sheet: -0.32 (0.48), residues: 106 loop : -0.58 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 93 HIS 0.004 0.001 HIS A 222 PHE 0.031 0.002 PHE A 428 TYR 0.016 0.002 TYR B 47 ARG 0.005 0.001 ARG B 187 *********************** 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 126 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2003 time to fit residues: 34.4583 Evaluate side-chains 89 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8547 ------------------------------------------------------------------------------- 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: 0.5980 chunk 71 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 6 optimal weight: 0.0970 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 18 optimal weight: 0.0000 chunk 57 optimal weight: 0.0770 chunk 9 optimal weight: 0.1980 overall best weight: 0.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7084 Z= 0.167 Angle : 0.593 6.576 9773 Z= 0.298 Chirality : 0.040 0.173 1109 Planarity : 0.005 0.040 1139 Dihedral : 16.610 151.444 1434 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 (0.33), residues: 265 sheet: -0.34 (0.50), residues: 102 loop : -0.51 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 409 HIS 0.007 0.001 HIS B 347 PHE 0.024 0.002 PHE A 371 TYR 0.010 0.001 TYR A 230 ARG 0.006 0.000 ARG B 187 ********************** 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 117 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1559 time to fit residues: 26.0121 Evaluate side-chains 99 residues out of total 644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.667 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 3 optimal weight: 0.0370 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.170939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.142453 restraints weight = 9788.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.145930 restraints weight = 6066.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.148356 restraints weight = 4316.985| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7084 Z= 0.304 Angle : 0.655 7.063 9773 Z= 0.332 Chirality : 0.042 0.194 1109 Planarity : 0.005 0.043 1139 Dihedral : 16.817 152.258 1434 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -0.11 (0.30), residues: 751 helix: 0.69 (0.32), residues: 264 sheet: -0.13 (0.54), residues: 102 loop : -0.53 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 409 HIS 0.007 0.001 HIS B 347 PHE 0.019 0.002 PHE A 371 TYR 0.013 0.002 TYR B 45 ARG 0.006 0.001 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1696.26 seconds wall clock time: 31 minutes 51.02 seconds (1911.02 seconds total)