Starting phenix.real_space_refine (version: dev) on Fri Feb 17 21:02:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2023/6vrl_21370_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2023/6vrl_21370.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2023/6vrl_21370_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2023/6vrl_21370_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2023/6vrl_21370_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2023/6vrl_21370.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2023/6vrl_21370.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2023/6vrl_21370_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vrl_21370/02_2023/6vrl_21370_updated.pdb" } resolution = 3.8 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= -0.001 sd= 0.971 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ASP 98": "OD1" <-> "OD2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A TYR 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 360": "OD1" <-> "OD2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A ASP 393": "OD1" <-> "OD2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A ASP 452": "OD1" <-> "OD2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A PHE 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 90": "OD1" <-> "OD2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 125": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 109": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4311 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 23, 'TRANS': 517} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 3, 'TRANS': 100} Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 924 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 5, 'TRANS': 111} Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 87 Unusual residues: {'LMT': 1, 'NAG': 2, 'RFY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 4.05, per 1000 atoms: 0.66 Number of scatterers: 6141 At special positions: 0 Unit cell: (95.256, 104.328, 82.296, 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) I 1 52.95 S 34 16.00 O 1103 8.00 N 958 7.00 C 4045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 701 " - " ASN A 208 " " NAG A 702 " - " ASN A 217 " Time building additional restraints: 2.94 Conformation dependent library (CDL) restraints added in 1.1 seconds 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1406 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 5 sheets defined 46.5% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 85 through 96 Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.740A pdb=" N LEU A 118 " --> pdb=" O GLY A 115 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 3.865A pdb=" N PHE A 127 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Processing helix chain 'A' and resid 156 through 189 removed outlier: 3.740A pdb=" N LYS A 159 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N GLY A 160 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE A 161 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N TYR A 176 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASN A 177 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 254 through 269 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.721A pdb=" N LYS A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N VAL A 283 " --> pdb=" O LYS A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 299 Processing helix chain 'A' and resid 306 through 313 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 344 through 348 Processing helix chain 'A' and resid 357 through 389 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 409 through 416 Processing helix chain 'A' and resid 420 through 453 removed outlier: 3.764A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 480 removed outlier: 4.751A pdb=" N VAL A 479 " --> pdb=" O PHE A 475 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N THR A 480 " --> pdb=" O GLY A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 495 Processing helix chain 'A' and resid 498 through 513 Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 535 through 542 Processing helix chain 'A' and resid 544 through 558 removed outlier: 3.531A pdb=" N MET A 558 " --> pdb=" O CYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 595 removed outlier: 4.254A pdb=" N SER A 585 " --> pdb=" O ILE A 581 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N PHE A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N CYS A 588 " --> pdb=" O SER A 584 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ILE A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) Proline residue: A 590 - end of helix Processing helix chain 'A' and resid 604 through 610 Processing sheet with id= A, first strand: chain 'C' and resid 24 through 26 removed outlier: 3.525A pdb=" N CYS C 43 " --> pdb=" O PHE C 91 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE C 91 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 105 through 110 removed outlier: 6.006A pdb=" N GLN C 57 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU C 66 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 22 through 25 Processing sheet with id= D, first strand: chain 'B' and resid 37 through 39 removed outlier: 3.811A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 102 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE B 39 " --> pdb=" O MET B 100 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET B 100 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 112 through 118 removed outlier: 3.750A pdb=" N VAL B 112 " --> pdb=" O GLN B 58 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 53 " --> pdb=" O ILE B 70 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE B 70 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LYS B 57 " --> pdb=" O TRP B 66 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N TRP B 66 " --> pdb=" O LYS B 57 " (cutoff:3.500A) 264 hydrogen bonds defined for protein. 675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.81 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 2681 1.40 - 1.58: 3595 1.58 - 1.75: 0 1.75 - 1.93: 49 1.93 - 2.11: 1 Bond restraints: 6326 Sorted by residual: bond pdb=" C06 RFY A 704 " pdb=" C07 RFY A 704 " ideal model delta sigma weight residual 1.512 1.576 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C04 RFY A 704 " pdb=" N03 RFY A 704 " ideal model delta sigma weight residual 1.445 1.492 -0.047 2.00e-02 2.50e+03 5.50e+00 bond pdb=" C02 RFY A 704 " pdb=" N03 RFY A 704 " ideal model delta sigma weight residual 1.450 1.492 -0.042 2.00e-02 2.50e+03 4.44e+00 bond pdb=" C05 RFY A 704 " pdb=" C06 RFY A 704 " ideal model delta sigma weight residual 1.531 1.493 0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" C01 RFY A 704 " pdb=" C06 RFY A 704 " ideal model delta sigma weight residual 1.527 1.498 0.029 2.00e-02 2.50e+03 2.17e+00 ... (remaining 6321 not shown) Histogram of bond angle deviations from ideal: 100.18 - 106.95: 184 106.95 - 113.71: 3435 113.71 - 120.48: 2531 120.48 - 127.24: 2385 127.24 - 134.01: 84 Bond angle restraints: 8619 Sorted by residual: angle pdb=" N VAL A 397 " pdb=" CA VAL A 397 " pdb=" C VAL A 397 " ideal model delta sigma weight residual 113.42 109.33 4.09 1.17e+00 7.31e-01 1.22e+01 angle pdb=" N ARG B 121 " pdb=" CA ARG B 121 " pdb=" C ARG B 121 " ideal model delta sigma weight residual 109.81 117.12 -7.31 2.21e+00 2.05e-01 1.09e+01 angle pdb=" C VAL B 120 " pdb=" N ARG B 121 " pdb=" CA ARG B 121 " ideal model delta sigma weight residual 121.80 128.79 -6.99 2.44e+00 1.68e-01 8.20e+00 angle pdb=" CA VAL A 397 " pdb=" C VAL A 397 " pdb=" N ALA A 398 " ideal model delta sigma weight residual 118.90 116.76 2.14 9.40e-01 1.13e+00 5.20e+00 angle pdb=" C01 RFY A 704 " pdb=" C06 RFY A 704 " pdb=" C05 RFY A 704 " ideal model delta sigma weight residual 107.15 113.59 -6.44 3.00e+00 1.11e-01 4.61e+00 ... (remaining 8614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.02: 3338 22.02 - 44.05: 228 44.05 - 66.07: 20 66.07 - 88.09: 3 88.09 - 110.12: 2 Dihedral angle restraints: 3591 sinusoidal: 1377 harmonic: 2214 Sorted by residual: dihedral pdb=" CA ARG B 121 " pdb=" C ARG B 121 " pdb=" N PRO B 122 " pdb=" CA PRO B 122 " ideal model delta harmonic sigma weight residual 180.00 128.14 51.86 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CB CYS A 200 " pdb=" SG CYS A 200 " pdb=" SG CYS A 209 " pdb=" CB CYS A 209 " ideal model delta sinusoidal sigma weight residual 93.00 133.61 -40.61 1 1.00e+01 1.00e-02 2.31e+01 dihedral pdb=" C01 RFY A 704 " pdb=" C02 RFY A 704 " pdb=" N03 RFY A 704 " pdb=" C04 RFY A 704 " ideal model delta sinusoidal sigma weight residual -53.70 56.42 -110.12 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 3588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 582 0.028 - 0.056: 261 0.056 - 0.084: 85 0.084 - 0.112: 32 0.112 - 0.140: 6 Chirality restraints: 966 Sorted by residual: chirality pdb=" CB ILE A 553 " pdb=" CA ILE A 553 " pdb=" CG1 ILE A 553 " pdb=" CG2 ILE A 553 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.88e-01 chirality pdb=" CA ILE C 114 " pdb=" N ILE C 114 " pdb=" C ILE C 114 " pdb=" CB ILE C 114 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA VAL B 91 " pdb=" N VAL B 91 " pdb=" C VAL B 91 " pdb=" CB VAL B 91 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 963 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 121 " -0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO B 122 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 122 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 122 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 465 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.90e+00 pdb=" C PHE A 465 " 0.034 2.00e-02 2.50e+03 pdb=" O PHE A 465 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 466 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 589 " 0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 590 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 590 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 590 " 0.017 5.00e-02 4.00e+02 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.72: 265 2.72 - 3.28: 6934 3.28 - 3.84: 11086 3.84 - 4.40: 13089 4.40 - 4.96: 22141 Nonbonded interactions: 53515 Sorted by model distance: nonbonded pdb=" OG1 THR C 83 " pdb=" O THR C 94 " model vdw 2.159 2.440 nonbonded pdb=" OG SER B 110 " pdb=" O LEU B 134 " model vdw 2.173 2.440 nonbonded pdb=" O THR A 221 " pdb=" OG SER A 224 " model vdw 2.202 2.440 nonbonded pdb=" O ASP C 102 " pdb=" OH TYR C 106 " model vdw 2.235 2.440 nonbonded pdb=" O SER A 559 " pdb=" O6' LMT A 703 " model vdw 2.267 2.440 ... (remaining 53510 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 34 5.16 5 C 4045 2.51 5 N 958 2.21 5 O 1103 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 15.670 Check model and map are aligned: 0.100 Process input model: 21.230 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.002 0.064 6326 Z= 0.164 Angle : 0.556 7.308 8619 Z= 0.311 Chirality : 0.037 0.140 966 Planarity : 0.004 0.067 1048 Dihedral : 14.016 110.118 2176 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -3.12 (0.27), residues: 758 helix: -0.96 (0.24), residues: 360 sheet: -3.12 (0.42), residues: 99 loop : -3.02 (0.32), residues: 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1871 time to fit residues: 50.7563 Evaluate side-chains 146 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.727 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 6326 Z= 0.183 Angle : 0.624 9.237 8619 Z= 0.309 Chirality : 0.040 0.257 966 Planarity : 0.005 0.070 1048 Dihedral : 5.161 50.342 860 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -2.01 (0.30), residues: 758 helix: 0.08 (0.27), residues: 356 sheet: -2.86 (0.42), residues: 105 loop : -2.46 (0.35), residues: 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 162 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 165 average time/residue: 0.1657 time to fit residues: 37.3121 Evaluate side-chains 155 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0689 time to fit residues: 2.2935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 60 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 6326 Z= 0.173 Angle : 0.601 11.185 8619 Z= 0.297 Chirality : 0.039 0.186 966 Planarity : 0.004 0.070 1048 Dihedral : 4.809 51.111 860 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.60 (0.30), residues: 758 helix: 0.33 (0.28), residues: 352 sheet: -2.42 (0.44), residues: 100 loop : -2.21 (0.35), residues: 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 158 average time/residue: 0.1698 time to fit residues: 37.0821 Evaluate side-chains 145 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.721 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0745 time to fit residues: 1.3927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 0.0370 chunk 64 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 6326 Z= 0.236 Angle : 0.638 10.727 8619 Z= 0.320 Chirality : 0.041 0.153 966 Planarity : 0.004 0.072 1048 Dihedral : 5.141 53.076 860 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.59 (0.30), residues: 758 helix: 0.20 (0.27), residues: 354 sheet: -2.45 (0.43), residues: 101 loop : -2.02 (0.36), residues: 303 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 17 residues processed: 156 average time/residue: 0.1743 time to fit residues: 37.0035 Evaluate side-chains 157 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.750 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0883 time to fit residues: 3.3800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 53 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 overall best weight: 1.0792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.3080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.193 Angle : 0.616 10.064 8619 Z= 0.307 Chirality : 0.040 0.144 966 Planarity : 0.004 0.072 1048 Dihedral : 5.027 52.336 860 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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 (0.30), residues: 758 helix: 0.34 (0.27), residues: 349 sheet: -2.34 (0.43), residues: 102 loop : -1.85 (0.36), residues: 307 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 142 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 151 average time/residue: 0.1692 time to fit residues: 34.5244 Evaluate side-chains 145 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 135 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0736 time to fit residues: 2.3007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 0.2980 chunk 72 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 6326 Z= 0.399 Angle : 0.770 10.860 8619 Z= 0.391 Chirality : 0.046 0.181 966 Planarity : 0.005 0.076 1048 Dihedral : 6.030 58.075 860 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 22.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer Outliers : 4.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.69 (0.30), residues: 758 helix: -0.05 (0.26), residues: 350 sheet: -2.71 (0.43), residues: 98 loop : -1.73 (0.37), residues: 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 0.754 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 157 average time/residue: 0.1626 time to fit residues: 34.9457 Evaluate side-chains 156 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.660 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0774 time to fit residues: 3.4591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 52 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 chunk 44 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 6326 Z= 0.194 Angle : 0.659 12.097 8619 Z= 0.329 Chirality : 0.040 0.145 966 Planarity : 0.004 0.072 1048 Dihedral : 5.355 54.672 860 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.39 (0.30), residues: 758 helix: 0.22 (0.27), residues: 355 sheet: -2.30 (0.42), residues: 106 loop : -1.70 (0.37), residues: 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 149 average time/residue: 0.1621 time to fit residues: 33.1467 Evaluate side-chains 140 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.686 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0783 time to fit residues: 1.4439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 63 optimal weight: 0.0770 chunk 67 optimal weight: 0.8980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 6326 Z= 0.210 Angle : 0.667 11.823 8619 Z= 0.333 Chirality : 0.041 0.150 966 Planarity : 0.004 0.073 1048 Dihedral : 5.368 55.490 860 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 18.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.19 (0.30), residues: 758 helix: 0.40 (0.27), residues: 348 sheet: -2.01 (0.44), residues: 102 loop : -1.68 (0.37), residues: 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 147 average time/residue: 0.1814 time to fit residues: 36.2731 Evaluate side-chains 146 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0659 time to fit residues: 1.7985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 6326 Z= 0.237 Angle : 0.686 10.254 8619 Z= 0.345 Chirality : 0.042 0.154 966 Planarity : 0.004 0.071 1048 Dihedral : 5.490 56.111 860 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.21 (0.30), residues: 758 helix: 0.37 (0.27), residues: 347 sheet: -1.81 (0.45), residues: 98 loop : -1.76 (0.36), residues: 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 0.768 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 145 average time/residue: 0.1626 time to fit residues: 32.8597 Evaluate side-chains 138 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 0.673 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0652 time to fit residues: 1.6133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.194 Angle : 0.656 11.681 8619 Z= 0.330 Chirality : 0.041 0.140 966 Planarity : 0.004 0.070 1048 Dihedral : 5.333 54.080 860 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.18 (0.30), residues: 758 helix: 0.34 (0.27), residues: 347 sheet: -1.54 (0.47), residues: 94 loop : -1.79 (0.36), residues: 317 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 142 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 144 average time/residue: 0.2075 time to fit residues: 41.5964 Evaluate side-chains 140 residues out of total 652 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.761 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1519 time to fit residues: 1.8810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS ** A 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.186885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.169937 restraints weight = 10277.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.173769 restraints weight = 6208.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.175998 restraints weight = 4163.169| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 6326 Z= 0.189 Angle : 0.661 11.011 8619 Z= 0.334 Chirality : 0.042 0.223 966 Planarity : 0.004 0.070 1048 Dihedral : 5.300 54.769 860 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.14 % Twisted Proline : 3.12 % 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: -1.10 (0.30), residues: 758 helix: 0.36 (0.28), residues: 345 sheet: -1.41 (0.48), residues: 96 loop : -1.69 (0.36), residues: 317 =============================================================================== Job complete usr+sys time: 1755.75 seconds wall clock time: 33 minutes 2.60 seconds (1982.60 seconds total)