Starting phenix.real_space_refine on Mon Mar 11 16:49:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b71_15895/03_2024/8b71_15895_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b71_15895/03_2024/8b71_15895.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b71_15895/03_2024/8b71_15895.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b71_15895/03_2024/8b71_15895.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b71_15895/03_2024/8b71_15895_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b71_15895/03_2024/8b71_15895_updated.pdb" } resolution = 3.8 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= 0.004 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 4 5.49 5 S 34 5.16 5 C 5766 2.51 5 N 1406 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 283": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A ARG 519": "NH1" <-> "NH2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ARG 331": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 467": "OE1" <-> "OE2" Residue "B ARG 519": "NH1" <-> "NH2" Residue "B GLU 521": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8694 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4303 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 23, 'TRANS': 528} Chain breaks: 2 Chain: "B" Number of atoms: 4303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4303 Classifications: {'peptide': 552} Link IDs: {'PTRANS': 23, 'TRANS': 528} Chain breaks: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Classifications: {'RNA': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Classifications: {'RNA': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.59 Number of scatterers: 8694 At special positions: 0 Unit cell: (113.847, 88.917, 98.889, 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 4 15.00 O 1484 8.00 N 1406 7.00 C 5766 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: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 2 sheets defined 70.7% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 31 through 53 removed outlier: 6.235A pdb=" N ASP A 36 " --> pdb=" O MET A 32 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA A 37 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N GLU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 87 removed outlier: 3.651A pdb=" N TRP A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 104 through 136 Processing helix chain 'A' and resid 138 through 142 removed outlier: 4.219A pdb=" N ASP A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 172 through 192 Processing helix chain 'A' and resid 216 through 228 removed outlier: 4.326A pdb=" N ALA A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 237 removed outlier: 3.759A pdb=" N ILE A 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 275 Processing helix chain 'A' and resid 285 through 294 Processing helix chain 'A' and resid 298 through 332 Proline residue: A 323 - end of helix removed outlier: 4.046A pdb=" N ASP A 332 " --> pdb=" O ASN A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 370 through 398 Proline residue: A 375 - end of helix Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 404 through 428 Processing helix chain 'A' and resid 430 through 462 Proline residue: A 435 - end of helix Proline residue: A 441 - end of helix Processing helix chain 'A' and resid 485 through 497 Processing helix chain 'A' and resid 510 through 522 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 583 through 590 Processing helix chain 'B' and resid 31 through 53 removed outlier: 6.235A pdb=" N ASP B 36 " --> pdb=" O MET B 32 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ALA B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR B 43 " --> pdb=" O SER B 39 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 87 removed outlier: 3.651A pdb=" N TRP B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 96 through 100 Processing helix chain 'B' and resid 104 through 136 Processing helix chain 'B' and resid 138 through 142 removed outlier: 4.220A pdb=" N ASP B 142 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 160 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 172 through 192 Processing helix chain 'B' and resid 216 through 228 removed outlier: 4.326A pdb=" N ALA B 228 " --> pdb=" O SER B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 removed outlier: 3.759A pdb=" N ILE B 235 " --> pdb=" O VAL B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 275 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 298 through 332 Proline residue: B 323 - end of helix removed outlier: 4.047A pdb=" N ASP B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 348 through 364 Processing helix chain 'B' and resid 370 through 398 Proline residue: B 375 - end of helix Proline residue: B 384 - end of helix Processing helix chain 'B' and resid 404 through 428 Processing helix chain 'B' and resid 430 through 462 Proline residue: B 435 - end of helix Proline residue: B 441 - end of helix Processing helix chain 'B' and resid 485 through 497 Processing helix chain 'B' and resid 510 through 522 Processing helix chain 'B' and resid 541 through 556 Processing helix chain 'B' and resid 583 through 590 Processing sheet with id= A, first strand: chain 'A' and resid 529 through 533 removed outlier: 7.790A pdb=" N VAL A 530 " --> pdb=" O VAL A 501 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A 503 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU A 532 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS A 505 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N ILE A 502 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL A 476 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL A 504 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL A 478 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 8.569A pdb=" N VAL A 506 " --> pdb=" O VAL A 478 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N SER A 560 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE A 477 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N MET A 562 " --> pdb=" O ILE A 477 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU A 564 " --> pdb=" O PRO A 479 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET A 597 " --> pdb=" O VAL A 563 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'B' and resid 529 through 533 removed outlier: 7.790A pdb=" N VAL B 530 " --> pdb=" O VAL B 501 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA B 503 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU B 532 " --> pdb=" O ALA B 503 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N HIS B 505 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE B 502 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N VAL B 476 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 504 " --> pdb=" O VAL B 476 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N VAL B 478 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N VAL B 506 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER B 560 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE B 477 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N MET B 562 " --> pdb=" O ILE B 477 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU B 564 " --> pdb=" O PRO B 479 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N MET B 597 " --> pdb=" O VAL B 563 " (cutoff:3.500A) No H-bonds generated for sheet with id= B 554 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2593 1.34 - 1.46: 1744 1.46 - 1.57: 4503 1.57 - 1.69: 8 1.69 - 1.81: 62 Bond restraints: 8910 Sorted by residual: bond pdb="C3'1 2BA A1001 " pdb="O3'1 2BA A1001 " ideal model delta sigma weight residual 1.418 1.344 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb="C3'1 2BA B 901 " pdb="O3'1 2BA B 901 " ideal model delta sigma weight residual 1.418 1.345 0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" C5' 2BA A1001 " pdb=" O5' 2BA A1001 " ideal model delta sigma weight residual 1.433 1.365 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C5' 2BA B 901 " pdb=" O5' 2BA B 901 " ideal model delta sigma weight residual 1.433 1.365 0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C3' 2BA B 901 " pdb=" O3' 2BA B 901 " ideal model delta sigma weight residual 1.410 1.352 0.058 2.00e-02 2.50e+03 8.54e+00 ... (remaining 8905 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.03: 175 105.03 - 112.30: 4731 112.30 - 119.57: 2782 119.57 - 126.84: 4316 126.84 - 134.11: 126 Bond angle restraints: 12130 Sorted by residual: angle pdb=" C2' 2BA A1001 " pdb=" C3' 2BA A1001 " pdb=" O3' 2BA A1001 " ideal model delta sigma weight residual 117.41 108.88 8.53 3.00e+00 1.11e-01 8.08e+00 angle pdb=" C2' 2BA B 901 " pdb=" C3' 2BA B 901 " pdb=" O3' 2BA B 901 " ideal model delta sigma weight residual 117.41 108.91 8.50 3.00e+00 1.11e-01 8.03e+00 angle pdb=" O1P 2BA A1001 " pdb=" P 2BA A1001 " pdb=" O2P 2BA A1001 " ideal model delta sigma weight residual 121.18 129.06 -7.88 3.00e+00 1.11e-01 6.89e+00 angle pdb=" O1P 2BA B 901 " pdb=" P 2BA B 901 " pdb=" O2P 2BA B 901 " ideal model delta sigma weight residual 121.18 128.98 -7.80 3.00e+00 1.11e-01 6.77e+00 angle pdb=" C LYS A 572 " pdb=" N ARG A 573 " pdb=" CA ARG A 573 " ideal model delta sigma weight residual 121.54 126.46 -4.92 1.91e+00 2.74e-01 6.63e+00 ... (remaining 12125 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.65: 5170 34.65 - 69.31: 110 69.31 - 103.96: 14 103.96 - 138.61: 2 138.61 - 173.26: 8 Dihedral angle restraints: 5304 sinusoidal: 2102 harmonic: 3202 Sorted by residual: dihedral pdb=" C5' 2BA B 901 " pdb=" O5' 2BA B 901 " pdb=" P 2BA B 901 " pdb=" O1P 2BA B 901 " ideal model delta sinusoidal sigma weight residual 191.97 18.71 173.26 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C5' 2BA A1001 " pdb=" O5' 2BA A1001 " pdb=" P 2BA A1001 " pdb=" O1P 2BA A1001 " ideal model delta sinusoidal sigma weight residual 191.97 18.79 173.18 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb="C5'1 2BA B 901 " pdb=" P1 2BA B 901 " pdb="O5'1 2BA B 901 " pdb="O2P1 2BA B 901 " ideal model delta sinusoidal sigma weight residual 30.08 -142.04 172.12 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1251 0.062 - 0.124: 187 0.124 - 0.186: 14 0.186 - 0.248: 0 0.248 - 0.310: 2 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C4' 2BA B 901 " pdb=" C3' 2BA B 901 " pdb=" C5' 2BA B 901 " pdb=" O4' 2BA B 901 " both_signs ideal model delta sigma weight residual False -2.39 -2.70 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C4' 2BA A1001 " pdb=" C3' 2BA A1001 " pdb=" C5' 2BA A1001 " pdb=" O4' 2BA A1001 " both_signs ideal model delta sigma weight residual False -2.39 -2.70 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CA TYR B 81 " pdb=" N TYR B 81 " pdb=" C TYR B 81 " pdb=" CB TYR B 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.71e-01 ... (remaining 1451 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 280 " 0.040 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO B 281 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 281 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 281 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 280 " -0.040 5.00e-02 4.00e+02 6.14e-02 6.03e+00 pdb=" N PRO A 281 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 281 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 281 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 88 " -0.038 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO B 89 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 89 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 89 " -0.032 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 154 2.68 - 3.24: 9187 3.24 - 3.79: 14493 3.79 - 4.35: 18861 4.35 - 4.90: 30536 Nonbonded interactions: 73231 Sorted by model distance: nonbonded pdb=" OG1 THR B 277 " pdb=" OE1 GLN B 288 " model vdw 2.129 2.440 nonbonded pdb=" OG1 THR A 277 " pdb=" OE1 GLN A 288 " model vdw 2.129 2.440 nonbonded pdb=" OG SER A 127 " pdb=" O GLY A 368 " model vdw 2.318 2.440 nonbonded pdb=" OG SER B 127 " pdb=" O GLY B 368 " model vdw 2.318 2.440 nonbonded pdb=" OG1 THR A 284 " pdb=" OG SER A 287 " model vdw 2.328 2.440 ... (remaining 73226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.470 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.040 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 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 : 0.005 0.074 8910 Z= 0.352 Angle : 0.708 8.529 12130 Z= 0.353 Chirality : 0.045 0.310 1454 Planarity : 0.005 0.062 1458 Dihedral : 17.410 173.263 3240 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 1092 helix: 1.16 (0.20), residues: 768 sheet: -0.30 (0.60), residues: 84 loop : -1.59 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 404 HIS 0.002 0.001 HIS A 141 PHE 0.015 0.001 PHE B 319 TYR 0.013 0.001 TYR A 43 ARG 0.002 0.000 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 0.973 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1832 time to fit residues: 40.5191 Evaluate side-chains 128 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 HIS B 372 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.0629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8910 Z= 0.214 Angle : 0.569 7.477 12130 Z= 0.289 Chirality : 0.040 0.164 1454 Planarity : 0.005 0.053 1458 Dihedral : 16.458 177.406 1296 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.22 % Allowed : 10.56 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.27), residues: 1092 helix: 1.27 (0.19), residues: 774 sheet: -0.27 (0.61), residues: 84 loop : -1.53 (0.44), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 404 HIS 0.002 0.001 HIS A 141 PHE 0.010 0.001 PHE A 591 TYR 0.015 0.001 TYR B 43 ARG 0.001 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 0.992 Fit side-chains REVERT: A 79 LEU cc_start: 0.8538 (mt) cc_final: 0.8281 (mt) REVERT: B 79 LEU cc_start: 0.8535 (mt) cc_final: 0.8275 (mt) outliers start: 2 outliers final: 0 residues processed: 141 average time/residue: 0.1770 time to fit residues: 36.2450 Evaluate side-chains 126 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 83 optimal weight: 0.2980 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8910 Z= 0.203 Angle : 0.547 7.361 12130 Z= 0.277 Chirality : 0.039 0.150 1454 Planarity : 0.005 0.052 1458 Dihedral : 16.196 177.410 1296 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.75 % Allowed : 13.47 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 1092 helix: 1.36 (0.19), residues: 772 sheet: -0.24 (0.62), residues: 84 loop : -1.49 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 404 HIS 0.002 0.000 HIS A 141 PHE 0.022 0.001 PHE B 591 TYR 0.008 0.001 TYR B 43 ARG 0.001 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 138 time to evaluate : 0.884 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 143 average time/residue: 0.1707 time to fit residues: 36.0364 Evaluate side-chains 135 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 459 GLU Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 95 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 604 HIS ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 604 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8910 Z= 0.192 Angle : 0.540 7.262 12130 Z= 0.273 Chirality : 0.038 0.120 1454 Planarity : 0.005 0.052 1458 Dihedral : 15.949 176.678 1296 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.62 % Allowed : 18.64 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1092 helix: 1.49 (0.19), residues: 772 sheet: -0.21 (0.61), residues: 84 loop : -1.49 (0.44), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 404 HIS 0.002 0.000 HIS A 141 PHE 0.015 0.001 PHE A 591 TYR 0.008 0.001 TYR B 273 ARG 0.001 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 0.975 Fit side-chains REVERT: A 477 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8460 (mt) REVERT: B 477 ILE cc_start: 0.8700 (OUTLIER) cc_final: 0.8487 (mt) outliers start: 15 outliers final: 9 residues processed: 147 average time/residue: 0.1690 time to fit residues: 36.7949 Evaluate side-chains 138 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 127 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 477 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8910 Z= 0.282 Angle : 0.604 8.153 12130 Z= 0.300 Chirality : 0.040 0.125 1454 Planarity : 0.005 0.052 1458 Dihedral : 15.845 169.499 1296 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.94 % Allowed : 19.83 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.27), residues: 1092 helix: 1.41 (0.19), residues: 766 sheet: -0.28 (0.61), residues: 84 loop : -1.32 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 404 HIS 0.002 0.001 HIS A 141 PHE 0.015 0.001 PHE A 591 TYR 0.011 0.001 TYR A 273 ARG 0.001 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.997 Fit side-chains REVERT: A 440 MET cc_start: 0.8706 (mmp) cc_final: 0.8464 (mmp) REVERT: A 477 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8424 (mt) REVERT: B 440 MET cc_start: 0.8677 (mmp) cc_final: 0.8439 (mmp) outliers start: 18 outliers final: 12 residues processed: 147 average time/residue: 0.1681 time to fit residues: 36.6529 Evaluate side-chains 139 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 126 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 121 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8910 Z= 0.217 Angle : 0.557 7.106 12130 Z= 0.280 Chirality : 0.039 0.123 1454 Planarity : 0.005 0.051 1458 Dihedral : 15.843 170.718 1296 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.62 % Allowed : 20.47 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1092 helix: 1.47 (0.19), residues: 766 sheet: -0.18 (0.61), residues: 84 loop : -1.33 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 404 HIS 0.002 0.000 HIS B 141 PHE 0.024 0.001 PHE B 591 TYR 0.009 0.001 TYR A 273 ARG 0.002 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.003 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 139 average time/residue: 0.1735 time to fit residues: 35.6270 Evaluate side-chains 134 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 124 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0870 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.0770 chunk 64 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8910 Z= 0.187 Angle : 0.547 6.921 12130 Z= 0.274 Chirality : 0.038 0.121 1454 Planarity : 0.005 0.052 1458 Dihedral : 15.977 174.963 1296 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.29 % Allowed : 21.34 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.27), residues: 1092 helix: 1.51 (0.19), residues: 766 sheet: -0.16 (0.61), residues: 84 loop : -1.35 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 404 HIS 0.001 0.000 HIS B 141 PHE 0.016 0.001 PHE A 565 TYR 0.007 0.001 TYR B 377 ARG 0.001 0.000 ARG B 589 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.926 Fit side-chains REVERT: A 85 ILE cc_start: 0.7857 (mp) cc_final: 0.7582 (mt) outliers start: 12 outliers final: 8 residues processed: 143 average time/residue: 0.1766 time to fit residues: 36.9193 Evaluate side-chains 138 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 499 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8910 Z= 0.204 Angle : 0.580 10.340 12130 Z= 0.285 Chirality : 0.039 0.140 1454 Planarity : 0.005 0.052 1458 Dihedral : 16.068 178.292 1296 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.19 % Allowed : 22.52 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.27), residues: 1092 helix: 1.46 (0.19), residues: 766 sheet: -0.19 (0.61), residues: 84 loop : -1.34 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 404 HIS 0.002 0.000 HIS A 141 PHE 0.007 0.001 PHE B 565 TYR 0.007 0.001 TYR A 273 ARG 0.001 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 0.866 Fit side-chains REVERT: A 396 TRP cc_start: 0.8026 (m100) cc_final: 0.7797 (m100) REVERT: A 547 LEU cc_start: 0.7776 (tp) cc_final: 0.7497 (mp) REVERT: B 396 TRP cc_start: 0.8032 (m100) cc_final: 0.7800 (m100) REVERT: B 547 LEU cc_start: 0.7750 (tp) cc_final: 0.7489 (mp) outliers start: 11 outliers final: 8 residues processed: 138 average time/residue: 0.1753 time to fit residues: 35.1235 Evaluate side-chains 138 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 499 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 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 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8910 Z= 0.207 Angle : 0.581 9.930 12130 Z= 0.286 Chirality : 0.039 0.126 1454 Planarity : 0.005 0.051 1458 Dihedral : 15.986 175.150 1296 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.51 % Allowed : 22.20 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 1092 helix: 1.45 (0.19), residues: 766 sheet: -0.27 (0.60), residues: 84 loop : -1.31 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 404 HIS 0.002 0.000 HIS B 141 PHE 0.008 0.001 PHE A 565 TYR 0.008 0.001 TYR A 81 ARG 0.001 0.000 ARG B 519 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 134 time to evaluate : 0.893 Fit side-chains REVERT: A 396 TRP cc_start: 0.8045 (m100) cc_final: 0.7794 (m100) REVERT: A 547 LEU cc_start: 0.7763 (tp) cc_final: 0.7503 (mp) REVERT: B 396 TRP cc_start: 0.8050 (m100) cc_final: 0.7800 (m100) REVERT: B 547 LEU cc_start: 0.7758 (tp) cc_final: 0.7499 (mp) outliers start: 14 outliers final: 10 residues processed: 144 average time/residue: 0.1687 time to fit residues: 35.5798 Evaluate side-chains 140 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 499 ASP Chi-restraints excluded: chain B residue 588 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.6980 chunk 72 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 92 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8910 Z= 0.188 Angle : 0.577 10.089 12130 Z= 0.283 Chirality : 0.038 0.117 1454 Planarity : 0.004 0.049 1458 Dihedral : 15.972 179.718 1296 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.86 % Allowed : 23.06 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.27), residues: 1092 helix: 1.53 (0.19), residues: 766 sheet: -0.18 (0.60), residues: 84 loop : -1.33 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 404 HIS 0.002 0.000 HIS B 141 PHE 0.008 0.001 PHE B 565 TYR 0.008 0.001 TYR A 81 ARG 0.002 0.000 ARG B 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 137 time to evaluate : 0.964 Fit side-chains REVERT: A 396 TRP cc_start: 0.8032 (m100) cc_final: 0.7785 (m100) REVERT: A 547 LEU cc_start: 0.7766 (tp) cc_final: 0.7509 (mp) REVERT: B 396 TRP cc_start: 0.8034 (m100) cc_final: 0.7792 (m100) REVERT: B 547 LEU cc_start: 0.7687 (tp) cc_final: 0.7420 (mp) outliers start: 8 outliers final: 8 residues processed: 141 average time/residue: 0.1840 time to fit residues: 37.5974 Evaluate side-chains 136 residues out of total 928 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 128 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 471 ILE Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 491 ILE Chi-restraints excluded: chain B residue 499 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 chunk 36 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 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 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 525 ASN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.163260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.148867 restraints weight = 9528.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.148677 restraints weight = 10711.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.148822 restraints weight = 9885.611| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8910 Z= 0.214 Angle : 0.600 9.875 12130 Z= 0.292 Chirality : 0.039 0.115 1454 Planarity : 0.005 0.050 1458 Dihedral : 15.932 179.294 1296 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.08 % Allowed : 23.81 % Favored : 75.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.27), residues: 1092 helix: 1.52 (0.19), residues: 766 sheet: -0.11 (0.61), residues: 84 loop : -1.29 (0.45), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 404 HIS 0.002 0.000 HIS B 141 PHE 0.008 0.001 PHE B 385 TYR 0.009 0.001 TYR A 81 ARG 0.001 0.000 ARG A 519 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1844.73 seconds wall clock time: 34 minutes 36.09 seconds (2076.09 seconds total)