Starting phenix.real_space_refine on Wed Feb 14 15:47:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/02_2024/7xf5_33169.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/02_2024/7xf5_33169.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/02_2024/7xf5_33169.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/02_2024/7xf5_33169.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/02_2024/7xf5_33169.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf5_33169/02_2024/7xf5_33169.pdb" } resolution = 3.9 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= 0.003 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 6294 2.51 5 N 1615 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 178": "OE1" <-> "OE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B GLU 320": "OE1" <-> "OE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 816": "OD1" <-> "OD2" Residue "B GLU 834": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9640 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 4837 Classifications: {'peptide': 622} Link IDs: {'PTRANS': 29, 'TRANS': 592} Chain breaks: 3 Chain: "B" Number of atoms: 4803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 617, 4803 Classifications: {'peptide': 617} Link IDs: {'PTRANS': 28, 'TRANS': 588} Chain breaks: 3 Time building chain proxies: 5.42, per 1000 atoms: 0.56 Number of scatterers: 9640 At special positions: 0 Unit cell: (111.915, 113.573, 116.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1674 8.00 N 1615 7.00 C 6294 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: 3.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 3 sheets defined 74.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 89 through 126 Processing helix chain 'A' and resid 129 through 156 Proline residue: A 141 - end of helix Processing helix chain 'A' and resid 157 through 160 Processing helix chain 'A' and resid 163 through 172 Processing helix chain 'A' and resid 176 through 180 Processing helix chain 'A' and resid 181 through 198 Processing helix chain 'A' and resid 204 through 225 Processing helix chain 'A' and resid 226 through 231 removed outlier: 6.910A pdb=" N ILE A 229 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR A 230 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 253 removed outlier: 3.609A pdb=" N PHE A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.614A pdb=" N SER A 267 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 296 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 320 through 352 removed outlier: 3.514A pdb=" N GLN A 352 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 364 through 378 removed outlier: 3.556A pdb=" N ALA A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.726A pdb=" N GLN A 385 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 419 through 425 Processing helix chain 'A' and resid 430 through 450 removed outlier: 4.142A pdb=" N TRP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 481 Processing helix chain 'A' and resid 495 through 513 removed outlier: 3.872A pdb=" N TYR A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 526 removed outlier: 4.425A pdb=" N VAL A 519 " --> pdb=" O VAL A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 549 Processing helix chain 'A' and resid 551 through 560 Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.828A pdb=" N TYR A 576 " --> pdb=" O HIS A 573 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 578 " --> pdb=" O GLN A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 596 through 607 removed outlier: 4.203A pdb=" N LEU A 600 " --> pdb=" O THR A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 640 removed outlier: 3.643A pdb=" N LEU A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 648 removed outlier: 3.706A pdb=" N ARG A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 778 removed outlier: 4.057A pdb=" N ILE A 771 " --> pdb=" O SER A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 814 removed outlier: 3.709A pdb=" N LEU A 813 " --> pdb=" O ILE A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 844 removed outlier: 4.120A pdb=" N LEU A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 126 removed outlier: 3.514A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 156 Proline residue: B 141 - end of helix Processing helix chain 'B' and resid 157 through 160 Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 176 through 180 Processing helix chain 'B' and resid 181 through 198 Processing helix chain 'B' and resid 204 through 225 removed outlier: 3.854A pdb=" N LEU B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 231 removed outlier: 7.085A pdb=" N ILE B 229 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR B 230 " --> pdb=" O GLY B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 253 removed outlier: 3.647A pdb=" N PHE B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 3.716A pdb=" N VAL B 259 " --> pdb=" O PRO B 255 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 267 " --> pdb=" O ILE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 296 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 320 through 352 Processing helix chain 'B' and resid 352 through 363 Processing helix chain 'B' and resid 364 through 378 removed outlier: 3.574A pdb=" N ALA B 368 " --> pdb=" O LEU B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.674A pdb=" N GLN B 385 " --> pdb=" O GLY B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 419 through 425 Processing helix chain 'B' and resid 430 through 450 removed outlier: 4.073A pdb=" N TRP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 481 Processing helix chain 'B' and resid 495 through 513 removed outlier: 3.866A pdb=" N TYR B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 526 Processing helix chain 'B' and resid 530 through 549 Processing helix chain 'B' and resid 551 through 560 Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.847A pdb=" N TYR B 576 " --> pdb=" O HIS B 573 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 578 " --> pdb=" O GLN B 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 584 removed outlier: 3.576A pdb=" N MET B 584 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 596 through 607 removed outlier: 3.867A pdb=" N LEU B 600 " --> pdb=" O THR B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 640 removed outlier: 3.751A pdb=" N LEU B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 648 removed outlier: 4.552A pdb=" N ARG B 645 " --> pdb=" O SER B 641 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS B 648 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 778 Processing helix chain 'B' and resid 802 through 810 Processing helix chain 'B' and resid 832 through 841 Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA2, first strand: chain 'A' and resid 485 through 487 Processing sheet with id=AA3, first strand: chain 'B' and resid 485 through 487 649 hydrogen bonds defined for protein. 1860 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: 2.87 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3038 1.34 - 1.46: 2194 1.46 - 1.58: 4533 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9861 Sorted by residual: bond pdb=" CA LEU B 812 " pdb=" C LEU B 812 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.34e-02 5.57e+03 4.52e+00 bond pdb=" CA LEU B 813 " pdb=" C LEU B 813 " ideal model delta sigma weight residual 1.521 1.503 0.018 1.36e-02 5.41e+03 1.71e+00 bond pdb=" N ILE B 170 " pdb=" CA ILE B 170 " ideal model delta sigma weight residual 1.461 1.447 0.014 1.19e-02 7.06e+03 1.34e+00 bond pdb=" C LYS B 168 " pdb=" O LYS B 168 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.19e-02 7.06e+03 1.30e+00 bond pdb=" C THR B 169 " pdb=" O THR B 169 " ideal model delta sigma weight residual 1.237 1.223 0.014 1.19e-02 7.06e+03 1.30e+00 ... (remaining 9856 not shown) Histogram of bond angle deviations from ideal: 98.16 - 105.35: 237 105.35 - 112.55: 5169 112.55 - 119.74: 3195 119.74 - 126.93: 4668 126.93 - 134.13: 130 Bond angle restraints: 13399 Sorted by residual: angle pdb=" N LEU B 813 " pdb=" CA LEU B 813 " pdb=" C LEU B 813 " ideal model delta sigma weight residual 113.41 99.84 13.57 1.22e+00 6.72e-01 1.24e+02 angle pdb=" N SER B 811 " pdb=" CA SER B 811 " pdb=" C SER B 811 " ideal model delta sigma weight residual 114.64 109.05 5.59 1.52e+00 4.33e-01 1.35e+01 angle pdb=" N PHE B 810 " pdb=" CA PHE B 810 " pdb=" C PHE B 810 " ideal model delta sigma weight residual 113.37 108.50 4.87 1.38e+00 5.25e-01 1.25e+01 angle pdb=" CB MET A 167 " pdb=" CG MET A 167 " pdb=" SD MET A 167 " ideal model delta sigma weight residual 112.70 104.08 8.62 3.00e+00 1.11e-01 8.26e+00 angle pdb=" C TYR B 230 " pdb=" N GLU B 231 " pdb=" CA GLU B 231 " ideal model delta sigma weight residual 121.94 116.23 5.71 2.00e+00 2.50e-01 8.16e+00 ... (remaining 13394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 5322 17.22 - 34.43: 377 34.43 - 51.65: 81 51.65 - 68.87: 27 68.87 - 86.08: 22 Dihedral angle restraints: 5829 sinusoidal: 2262 harmonic: 3567 Sorted by residual: dihedral pdb=" CB GLU B 166 " pdb=" CG GLU B 166 " pdb=" CD GLU B 166 " pdb=" OE1 GLU B 166 " ideal model delta sinusoidal sigma weight residual 0.00 -85.33 85.33 1 3.00e+01 1.11e-03 9.80e+00 dihedral pdb=" CA LEU B 813 " pdb=" CB LEU B 813 " pdb=" CG LEU B 813 " pdb=" CD1 LEU B 813 " ideal model delta sinusoidal sigma weight residual 60.00 116.27 -56.27 3 1.50e+01 4.44e-03 9.39e+00 dihedral pdb=" CG ARG A 558 " pdb=" CD ARG A 558 " pdb=" NE ARG A 558 " pdb=" CZ ARG A 558 " ideal model delta sinusoidal sigma weight residual -180.00 -138.50 -41.50 2 1.50e+01 4.44e-03 9.37e+00 ... (remaining 5826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1194 0.043 - 0.085: 298 0.085 - 0.127: 79 0.127 - 0.170: 5 0.170 - 0.212: 2 Chirality restraints: 1578 Sorted by residual: chirality pdb=" CA LEU B 813 " pdb=" N LEU B 813 " pdb=" C LEU B 813 " pdb=" CB LEU B 813 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA LEU B 812 " pdb=" N LEU B 812 " pdb=" C LEU B 812 " pdb=" CB LEU B 812 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA GLU B 231 " pdb=" N GLU B 231 " pdb=" C GLU B 231 " pdb=" CB GLU B 231 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 1575 not shown) Planarity restraints: 1671 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 444 " -0.019 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP A 444 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 444 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 444 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 444 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 444 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 444 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 444 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 444 " 0.012 2.00e-02 2.50e+03 1.25e-02 3.89e+00 pdb=" CG TRP B 444 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 444 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 444 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 444 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 444 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 444 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 444 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 379 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO B 380 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.022 5.00e-02 4.00e+02 ... (remaining 1668 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1459 2.76 - 3.29: 9581 3.29 - 3.83: 16013 3.83 - 4.36: 17154 4.36 - 4.90: 30157 Nonbonded interactions: 74364 Sorted by model distance: nonbonded pdb=" OE2 GLU A 320 " pdb=" OH TYR A 499 " model vdw 2.222 2.440 nonbonded pdb=" OE2 GLU B 320 " pdb=" OH TYR B 499 " model vdw 2.226 2.440 nonbonded pdb=" O GLU A 166 " pdb=" OG1 THR A 169 " model vdw 2.233 2.440 nonbonded pdb=" O ASP A 402 " pdb=" NH1 ARG A 471 " model vdw 2.284 2.520 nonbonded pdb=" O ARG B 601 " pdb=" ND1 HIS B 605 " model vdw 2.308 2.520 ... (remaining 74359 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' and (resid 89 through 649 or resid 769 through 845)) 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.920 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 27.770 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 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 : 0.003 0.045 9861 Z= 0.164 Angle : 0.607 13.571 13399 Z= 0.348 Chirality : 0.040 0.212 1578 Planarity : 0.004 0.040 1671 Dihedral : 14.141 86.085 3517 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.29 % Favored : 97.63 % Rotamer: Outliers : 0.58 % Allowed : 0.29 % Favored : 99.13 % 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: 1.11 (0.24), residues: 1223 helix: 1.51 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -0.93 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP A 444 HIS 0.012 0.001 HIS B 210 PHE 0.021 0.001 PHE B 147 TYR 0.016 0.001 TYR A 140 ARG 0.011 0.000 ARG B 277 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 344 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 HIS cc_start: 0.7891 (t-170) cc_final: 0.7565 (t70) REVERT: A 239 MET cc_start: 0.7214 (mmt) cc_final: 0.6759 (ptm) REVERT: A 309 ARG cc_start: 0.6994 (ttp-170) cc_final: 0.6200 (mtm110) REVERT: A 340 TYR cc_start: 0.6818 (t80) cc_final: 0.6472 (t80) REVERT: A 374 ILE cc_start: 0.8639 (tt) cc_final: 0.8155 (mt) REVERT: A 439 ILE cc_start: 0.8192 (mm) cc_final: 0.7980 (mt) REVERT: A 531 ILE cc_start: 0.9316 (tt) cc_final: 0.9045 (tt) REVERT: A 549 GLN cc_start: 0.7704 (tp-100) cc_final: 0.7359 (tt0) REVERT: A 558 ARG cc_start: 0.6490 (mmt180) cc_final: 0.5991 (mtt-85) REVERT: A 801 THR cc_start: 0.5389 (m) cc_final: 0.5177 (m) REVERT: B 219 LEU cc_start: 0.8581 (tp) cc_final: 0.8373 (tp) REVERT: B 374 ILE cc_start: 0.8657 (tt) cc_final: 0.8180 (mt) REVERT: B 558 ARG cc_start: 0.6348 (mmt180) cc_final: 0.5626 (mtt180) REVERT: B 815 VAL cc_start: 0.5453 (OUTLIER) cc_final: 0.5240 (m) outliers start: 6 outliers final: 1 residues processed: 347 average time/residue: 0.2257 time to fit residues: 105.9531 Evaluate side-chains 217 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 215 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 51 optimal weight: 30.0000 chunk 31 optimal weight: 0.0980 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 37 optimal weight: 0.2980 chunk 58 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 111 optimal weight: 7.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 133 GLN ** A 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 513 HIS A 546 GLN B 133 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9861 Z= 0.292 Angle : 0.655 7.737 13399 Z= 0.336 Chirality : 0.046 0.276 1578 Planarity : 0.005 0.046 1671 Dihedral : 4.298 48.912 1324 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.11 % Allowed : 8.93 % Favored : 87.96 % 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: 1.02 (0.24), residues: 1223 helix: 1.43 (0.17), residues: 839 sheet: None (None), residues: 0 loop : -0.96 (0.33), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 91 HIS 0.004 0.001 HIS B 210 PHE 0.024 0.002 PHE B 522 TYR 0.017 0.002 TYR B 134 ARG 0.011 0.001 ARG B 361 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 245 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.7186 (mmm) cc_final: 0.6973 (mmm) REVERT: A 309 ARG cc_start: 0.7249 (ttp-170) cc_final: 0.7020 (mtm110) REVERT: A 374 ILE cc_start: 0.8585 (tt) cc_final: 0.8223 (mt) REVERT: A 383 PHE cc_start: 0.8246 (t80) cc_final: 0.8019 (t80) REVERT: A 385 GLN cc_start: 0.8328 (pt0) cc_final: 0.7900 (pt0) REVERT: B 178 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.6015 (pm20) REVERT: B 214 MET cc_start: 0.7665 (mtp) cc_final: 0.7424 (mtp) REVERT: B 344 LYS cc_start: 0.7971 (mmtm) cc_final: 0.7730 (mmmm) REVERT: B 374 ILE cc_start: 0.8625 (tt) cc_final: 0.8413 (mt) REVERT: B 383 PHE cc_start: 0.8356 (t80) cc_final: 0.8062 (t80) REVERT: B 395 GLU cc_start: 0.7674 (pm20) cc_final: 0.7425 (mp0) outliers start: 32 outliers final: 21 residues processed: 262 average time/residue: 0.2162 time to fit residues: 78.4420 Evaluate side-chains 229 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 207 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 405 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 806 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 HIS B 133 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.4055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9861 Z= 0.185 Angle : 0.559 14.007 13399 Z= 0.279 Chirality : 0.042 0.167 1578 Planarity : 0.004 0.034 1671 Dihedral : 3.581 18.859 1321 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.43 % Allowed : 12.91 % Favored : 84.66 % 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: 1.40 (0.24), residues: 1223 helix: 1.72 (0.18), residues: 835 sheet: None (None), residues: 0 loop : -0.80 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 91 HIS 0.006 0.001 HIS B 807 PHE 0.015 0.001 PHE B 185 TYR 0.017 0.001 TYR A 140 ARG 0.003 0.000 ARG A 343 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 217 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5831 (m-80) cc_final: 0.5580 (m-80) REVERT: A 374 ILE cc_start: 0.8577 (tt) cc_final: 0.8227 (mt) REVERT: B 167 MET cc_start: 0.7190 (mmt) cc_final: 0.6977 (mmm) REVERT: B 344 LYS cc_start: 0.7955 (mmtm) cc_final: 0.7719 (mmmm) REVERT: B 374 ILE cc_start: 0.8571 (tt) cc_final: 0.8366 (mt) REVERT: B 395 GLU cc_start: 0.7619 (pm20) cc_final: 0.7395 (mp0) REVERT: B 523 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7196 (mt-10) outliers start: 25 outliers final: 18 residues processed: 229 average time/residue: 0.2249 time to fit residues: 71.9101 Evaluate side-chains 216 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 198 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 806 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 9.9990 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 32 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9861 Z= 0.186 Angle : 0.549 14.163 13399 Z= 0.274 Chirality : 0.041 0.172 1578 Planarity : 0.004 0.033 1671 Dihedral : 3.541 18.295 1321 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.62 % Allowed : 13.50 % Favored : 83.88 % 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: 1.52 (0.24), residues: 1223 helix: 1.84 (0.18), residues: 827 sheet: None (None), residues: 0 loop : -0.80 (0.32), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 444 HIS 0.005 0.001 HIS A 513 PHE 0.022 0.001 PHE B 279 TYR 0.014 0.001 TYR A 179 ARG 0.003 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 218 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5816 (m-80) cc_final: 0.5563 (m-80) REVERT: A 383 PHE cc_start: 0.8169 (t80) cc_final: 0.7908 (t80) REVERT: A 395 GLU cc_start: 0.7477 (pt0) cc_final: 0.7215 (tp30) REVERT: A 477 MET cc_start: 0.7655 (mmm) cc_final: 0.7434 (mmm) REVERT: B 167 MET cc_start: 0.7486 (mmt) cc_final: 0.7192 (mmm) REVERT: B 210 HIS cc_start: 0.8292 (t-90) cc_final: 0.7992 (t-90) REVERT: B 218 LEU cc_start: 0.7306 (tt) cc_final: 0.6278 (mt) REVERT: B 344 LYS cc_start: 0.8006 (mmtm) cc_final: 0.7729 (mmmm) REVERT: B 383 PHE cc_start: 0.8347 (t80) cc_final: 0.7993 (t80) outliers start: 27 outliers final: 22 residues processed: 230 average time/residue: 0.2266 time to fit residues: 72.4373 Evaluate side-chains 225 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 203 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 215 CYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 387 MET Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 806 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.0030 chunk 1 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 8.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 106 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 0.1980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 GLN B 422 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9861 Z= 0.161 Angle : 0.541 14.614 13399 Z= 0.265 Chirality : 0.041 0.179 1578 Planarity : 0.004 0.036 1671 Dihedral : 3.470 17.531 1321 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.33 % Allowed : 16.02 % Favored : 81.65 % 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: 1.68 (0.25), residues: 1223 helix: 1.95 (0.18), residues: 831 sheet: None (None), residues: 0 loop : -0.71 (0.33), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 444 HIS 0.005 0.001 HIS B 807 PHE 0.026 0.001 PHE B 289 TYR 0.012 0.001 TYR A 140 ARG 0.002 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 218 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5825 (m-80) cc_final: 0.5591 (m-80) REVERT: A 383 PHE cc_start: 0.8174 (t80) cc_final: 0.7912 (t80) REVERT: A 395 GLU cc_start: 0.7464 (pt0) cc_final: 0.7205 (tp30) REVERT: A 453 PRO cc_start: 0.8485 (Cg_endo) cc_final: 0.8259 (Cg_exo) REVERT: A 477 MET cc_start: 0.7639 (mmm) cc_final: 0.7397 (mmm) REVERT: B 178 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6039 (pm20) REVERT: B 218 LEU cc_start: 0.7321 (tt) cc_final: 0.6338 (mt) REVERT: B 344 LYS cc_start: 0.8009 (mmtm) cc_final: 0.7691 (mmmm) REVERT: B 383 PHE cc_start: 0.8247 (t80) cc_final: 0.7941 (t80) outliers start: 24 outliers final: 20 residues processed: 226 average time/residue: 0.2129 time to fit residues: 68.0728 Evaluate side-chains 225 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 178 GLU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 515 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 0.5980 chunk 55 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 39 optimal weight: 0.0980 chunk 62 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9861 Z= 0.175 Angle : 0.574 15.536 13399 Z= 0.280 Chirality : 0.041 0.188 1578 Planarity : 0.004 0.037 1671 Dihedral : 3.473 16.832 1321 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.52 % Allowed : 17.18 % Favored : 80.29 % 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: 1.72 (0.25), residues: 1223 helix: 1.96 (0.18), residues: 828 sheet: None (None), residues: 0 loop : -0.62 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 137 HIS 0.007 0.001 HIS B 807 PHE 0.020 0.001 PHE A 287 TYR 0.013 0.001 TYR A 340 ARG 0.002 0.000 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 213 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5839 (m-80) cc_final: 0.5594 (m-80) REVERT: A 383 PHE cc_start: 0.8225 (t80) cc_final: 0.7950 (t80) REVERT: B 218 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.6460 (mt) REVERT: B 232 ASN cc_start: 0.2687 (OUTLIER) cc_final: 0.1600 (m-40) REVERT: B 263 ILE cc_start: 0.8449 (mt) cc_final: 0.8123 (mm) REVERT: B 344 LYS cc_start: 0.8029 (mmtm) cc_final: 0.7706 (mmmm) REVERT: B 383 PHE cc_start: 0.8227 (t80) cc_final: 0.7932 (t80) REVERT: B 453 PRO cc_start: 0.8434 (Cg_endo) cc_final: 0.8189 (Cg_exo) outliers start: 26 outliers final: 23 residues processed: 223 average time/residue: 0.2228 time to fit residues: 70.3131 Evaluate side-chains 228 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9861 Z= 0.188 Angle : 0.568 15.263 13399 Z= 0.279 Chirality : 0.041 0.173 1578 Planarity : 0.004 0.048 1671 Dihedral : 3.498 16.875 1321 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.01 % Allowed : 17.96 % Favored : 79.03 % 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: 1.59 (0.25), residues: 1223 helix: 1.85 (0.18), residues: 833 sheet: None (None), residues: 0 loop : -0.67 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 121 HIS 0.006 0.001 HIS B 807 PHE 0.021 0.001 PHE A 287 TYR 0.013 0.001 TYR A 140 ARG 0.005 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 218 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 TRP cc_start: 0.7155 (t-100) cc_final: 0.6307 (t60) REVERT: A 314 PHE cc_start: 0.5846 (m-80) cc_final: 0.5615 (m-80) REVERT: A 383 PHE cc_start: 0.8277 (t80) cc_final: 0.7978 (t80) REVERT: B 218 LEU cc_start: 0.7290 (tt) cc_final: 0.6448 (mt) REVERT: B 235 ARG cc_start: 0.3037 (mtt-85) cc_final: 0.2001 (ttm110) REVERT: B 344 LYS cc_start: 0.8101 (mmtm) cc_final: 0.7756 (mmmm) REVERT: B 383 PHE cc_start: 0.8204 (t80) cc_final: 0.7878 (t80) outliers start: 31 outliers final: 26 residues processed: 233 average time/residue: 0.2498 time to fit residues: 80.9126 Evaluate side-chains 234 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9861 Z= 0.212 Angle : 0.591 17.439 13399 Z= 0.293 Chirality : 0.042 0.185 1578 Planarity : 0.004 0.048 1671 Dihedral : 3.598 18.345 1321 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.82 % Allowed : 18.25 % Favored : 78.93 % 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: 1.58 (0.25), residues: 1223 helix: 1.84 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -0.62 (0.33), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 121 HIS 0.006 0.001 HIS B 807 PHE 0.024 0.001 PHE B 287 TYR 0.015 0.001 TYR A 340 ARG 0.006 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 LEU cc_start: 0.8079 (mt) cc_final: 0.7867 (mm) REVERT: A 314 PHE cc_start: 0.5979 (m-80) cc_final: 0.5766 (m-80) REVERT: A 383 PHE cc_start: 0.8297 (t80) cc_final: 0.7931 (t80) REVERT: B 218 LEU cc_start: 0.7340 (tt) cc_final: 0.6528 (mt) REVERT: B 377 LEU cc_start: 0.8747 (mt) cc_final: 0.8545 (mp) REVERT: B 383 PHE cc_start: 0.8235 (t80) cc_final: 0.7884 (t80) REVERT: B 611 MET cc_start: 0.0871 (mmp) cc_final: 0.0658 (mtp) outliers start: 29 outliers final: 25 residues processed: 229 average time/residue: 0.2021 time to fit residues: 65.1919 Evaluate side-chains 228 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 203 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 348 VAL Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 348 VAL Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 110 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 66 optimal weight: 0.3980 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 116 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9861 Z= 0.174 Angle : 0.599 16.814 13399 Z= 0.288 Chirality : 0.041 0.177 1578 Planarity : 0.004 0.047 1671 Dihedral : 3.500 18.344 1321 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.52 % Allowed : 19.03 % Favored : 78.45 % 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: 1.60 (0.25), residues: 1223 helix: 1.85 (0.18), residues: 833 sheet: None (None), residues: 0 loop : -0.65 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 121 HIS 0.006 0.001 HIS B 807 PHE 0.026 0.001 PHE B 287 TYR 0.016 0.001 TYR A 140 ARG 0.003 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 219 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5954 (m-80) cc_final: 0.5747 (m-80) REVERT: A 383 PHE cc_start: 0.8285 (t80) cc_final: 0.7869 (t80) REVERT: B 218 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6539 (mt) REVERT: B 231 GLU cc_start: 0.1981 (OUTLIER) cc_final: 0.1664 (mm-30) REVERT: B 235 ARG cc_start: 0.3196 (mtt-85) cc_final: 0.2503 (ttm110) REVERT: B 383 PHE cc_start: 0.8208 (t80) cc_final: 0.7894 (t80) outliers start: 26 outliers final: 21 residues processed: 228 average time/residue: 0.2048 time to fit residues: 66.1313 Evaluate side-chains 231 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 208 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 231 GLU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 303 THR Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9861 Z= 0.214 Angle : 0.629 17.134 13399 Z= 0.303 Chirality : 0.043 0.209 1578 Planarity : 0.004 0.050 1671 Dihedral : 3.585 18.348 1321 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.23 % Allowed : 19.42 % Favored : 78.35 % 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: 1.49 (0.25), residues: 1223 helix: 1.75 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -0.66 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 91 HIS 0.008 0.001 HIS A 817 PHE 0.026 0.001 PHE B 287 TYR 0.016 0.001 TYR A 340 ARG 0.006 0.000 ARG A 273 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 314 PHE cc_start: 0.5923 (m-80) cc_final: 0.5589 (m-80) REVERT: A 383 PHE cc_start: 0.8290 (t80) cc_final: 0.7870 (t80) REVERT: B 218 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6528 (mt) REVERT: B 383 PHE cc_start: 0.8165 (t80) cc_final: 0.7818 (t80) REVERT: B 611 MET cc_start: 0.0900 (mmp) cc_final: 0.0692 (mtp) outliers start: 23 outliers final: 20 residues processed: 214 average time/residue: 0.2140 time to fit residues: 66.0893 Evaluate side-chains 222 residues out of total 1030 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 201 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 252 PHE Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 395 GLU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 621 MET Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 807 HIS Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 208 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 252 PHE Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 420 THR Chi-restraints excluded: chain B residue 421 SER Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 815 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.5980 chunk 89 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 ASN B 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.200480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.154502 restraints weight = 15729.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.158083 restraints weight = 8911.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.160455 restraints weight = 6233.173| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9861 Z= 0.178 Angle : 0.612 16.553 13399 Z= 0.295 Chirality : 0.042 0.179 1578 Planarity : 0.004 0.049 1671 Dihedral : 3.523 17.032 1321 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.52 % Allowed : 20.10 % Favored : 77.38 % 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: 1.54 (0.24), residues: 1223 helix: 1.79 (0.18), residues: 833 sheet: None (None), residues: 0 loop : -0.63 (0.33), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 137 HIS 0.005 0.001 HIS B 807 PHE 0.027 0.001 PHE B 287 TYR 0.014 0.001 TYR B 134 ARG 0.007 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.14 seconds wall clock time: 42 minutes 18.42 seconds (2538.42 seconds total)