Starting phenix.real_space_refine on Sat Feb 17 21:53:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdd_25825/02_2024/7tdd_25825.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdd_25825/02_2024/7tdd_25825.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdd_25825/02_2024/7tdd_25825.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdd_25825/02_2024/7tdd_25825.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdd_25825/02_2024/7tdd_25825.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tdd_25825/02_2024/7tdd_25825.pdb" } resolution = 3.5 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= 0.001 sd= 0.016 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 S 46 5.16 5 C 6690 2.51 5 N 1549 2.21 5 O 1721 1.98 5 H 10025 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 469": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20031 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 10006 Classifications: {'peptide': 605} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 586} Chain breaks: 5 Chain: "B" Number of atoms: 10025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 10025 Classifications: {'peptide': 606} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 587} Chain breaks: 5 Time building chain proxies: 9.49, per 1000 atoms: 0.47 Number of scatterers: 20031 At special positions: 0 Unit cell: (125.25, 99.365, 105.21, 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 46 16.00 O 1721 8.00 N 1549 7.00 C 6690 6.00 H 10025 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS B 93 " - pdb=" SG CYS B 101 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.56 Conformation dependent library (CDL) restraints added in 2.1 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 0 sheets defined 87.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 16 through 28 Processing helix chain 'A' and resid 29 through 43 Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 150 through 173 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.722A pdb=" N VAL A 192 " --> pdb=" O PRO A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.955A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.688A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 295 removed outlier: 4.070A pdb=" N PHE A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 333 removed outlier: 3.782A pdb=" N GLY A 318 " --> pdb=" O LYS A 314 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 319 " --> pdb=" O GLN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 411 through 416 removed outlier: 3.528A pdb=" N HIS A 416 " --> pdb=" O PRO A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 428 removed outlier: 3.823A pdb=" N GLN A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 451 Processing helix chain 'A' and resid 462 through 493 removed outlier: 3.960A pdb=" N VAL A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE A 488 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 8.894A pdb=" N GLU A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 515 Processing helix chain 'A' and resid 530 through 540 Processing helix chain 'A' and resid 541 through 547 removed outlier: 4.233A pdb=" N LEU A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 588 removed outlier: 4.213A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) Proline residue: A 563 - end of helix Proline residue: A 567 - end of helix Processing helix chain 'A' and resid 597 through 600 Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 615 through 629 Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.833A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 661 removed outlier: 4.183A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 690 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 29 through 43 Processing helix chain 'B' and resid 61 through 70 Processing helix chain 'B' and resid 70 through 88 removed outlier: 4.614A pdb=" N ASN B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N PHE B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 96 removed outlier: 3.620A pdb=" N ASN B 96 " --> pdb=" O CYS B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 137 Processing helix chain 'B' and resid 137 through 143 removed outlier: 4.544A pdb=" N TYR B 141 " --> pdb=" O PHE B 137 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY B 143 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 150 through 173 Processing helix chain 'B' and resid 186 through 199 removed outlier: 3.931A pdb=" N VAL B 192 " --> pdb=" O PRO B 188 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 199 " --> pdb=" O PHE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 212 removed outlier: 3.656A pdb=" N GLY B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 238 removed outlier: 4.008A pdb=" N ASN B 218 " --> pdb=" O GLY B 214 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 250 through 264 removed outlier: 3.508A pdb=" N THR B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 271 through 278 Processing helix chain 'B' and resid 280 through 295 removed outlier: 4.313A pdb=" N PHE B 284 " --> pdb=" O TRP B 280 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE B 285 " --> pdb=" O SER B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 333 Processing helix chain 'B' and resid 345 through 354 removed outlier: 4.369A pdb=" N LEU B 350 " --> pdb=" O GLN B 346 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 398 removed outlier: 3.612A pdb=" N LEU B 397 " --> pdb=" O GLN B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.657A pdb=" N HIS B 410 " --> pdb=" O LEU B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 417 Processing helix chain 'B' and resid 417 through 428 removed outlier: 3.984A pdb=" N GLN B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 455 Processing helix chain 'B' and resid 461 through 487 removed outlier: 3.793A pdb=" N PHE B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 470 " --> pdb=" O VAL B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 493 Processing helix chain 'B' and resid 494 through 515 removed outlier: 3.677A pdb=" N TRP B 505 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 540 Processing helix chain 'B' and resid 542 through 547 removed outlier: 3.754A pdb=" N MET B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 565 removed outlier: 4.270A pdb=" N PHE B 554 " --> pdb=" O ARG B 550 " (cutoff:3.500A) Proline residue: B 563 - end of helix Processing helix chain 'B' and resid 565 through 588 Processing helix chain 'B' and resid 597 through 600 Processing helix chain 'B' and resid 601 through 606 Processing helix chain 'B' and resid 615 through 629 Processing helix chain 'B' and resid 632 through 644 removed outlier: 3.801A pdb=" N MET B 636 " --> pdb=" O TRP B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' Processing helix chain 'B' and resid 648 through 660 removed outlier: 4.097A pdb=" N PHE B 652 " --> pdb=" O SER B 648 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 690 717 hydrogen bonds defined for protein. 2124 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: 7.26 Time building geometry restraints manager: 17.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 6804 1.02 - 1.22: 3234 1.22 - 1.42: 4881 1.42 - 1.61: 5312 1.61 - 1.81: 74 Bond restraints: 20305 Sorted by residual: bond pdb=" CB THR B 264 " pdb=" OG1 THR B 264 " ideal model delta sigma weight residual 1.433 1.269 0.164 1.60e-02 3.91e+03 1.05e+02 bond pdb=" CA ALA A 187 " pdb=" CB ALA A 187 " ideal model delta sigma weight residual 1.534 1.427 0.107 1.18e-02 7.18e+03 8.30e+01 bond pdb=" CA ALA B 187 " pdb=" CB ALA B 187 " ideal model delta sigma weight residual 1.534 1.427 0.107 1.18e-02 7.18e+03 8.27e+01 bond pdb=" CZ ARG B 191 " pdb=" NH2 ARG B 191 " ideal model delta sigma weight residual 1.330 1.227 0.103 1.30e-02 5.92e+03 6.23e+01 bond pdb=" CZ ARG A 191 " pdb=" NH2 ARG A 191 " ideal model delta sigma weight residual 1.330 1.228 0.102 1.30e-02 5.92e+03 6.21e+01 ... (remaining 20300 not shown) Histogram of bond angle deviations from ideal: 99.02 - 106.57: 2671 106.57 - 114.13: 20373 114.13 - 121.68: 10103 121.68 - 129.23: 3328 129.23 - 136.78: 115 Bond angle restraints: 36590 Sorted by residual: angle pdb=" N ILE A 272 " pdb=" CA ILE A 272 " pdb=" CB ILE A 272 " ideal model delta sigma weight residual 110.52 115.79 -5.27 6.70e-01 2.23e+00 6.19e+01 angle pdb=" CA PHE A 86 " pdb=" CB PHE A 86 " pdb=" CG PHE A 86 " ideal model delta sigma weight residual 113.80 121.62 -7.82 1.00e+00 1.00e+00 6.11e+01 angle pdb=" CA ASN B 618 " pdb=" CB ASN B 618 " pdb=" CG ASN B 618 " ideal model delta sigma weight residual 112.60 120.14 -7.54 1.00e+00 1.00e+00 5.69e+01 angle pdb=" CA ASN A 85 " pdb=" CB ASN A 85 " pdb=" CG ASN A 85 " ideal model delta sigma weight residual 112.60 120.13 -7.53 1.00e+00 1.00e+00 5.67e+01 angle pdb=" CA ASP B 166 " pdb=" CB ASP B 166 " pdb=" CG ASP B 166 " ideal model delta sigma weight residual 112.60 120.01 -7.41 1.00e+00 1.00e+00 5.50e+01 ... (remaining 36585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8826 17.77 - 35.54: 444 35.54 - 53.31: 133 53.31 - 71.08: 160 71.08 - 88.85: 9 Dihedral angle restraints: 9572 sinusoidal: 4945 harmonic: 4627 Sorted by residual: dihedral pdb=" C MET A 629 " pdb=" N MET A 629 " pdb=" CA MET A 629 " pdb=" CB MET A 629 " ideal model delta harmonic sigma weight residual -122.60 -140.24 17.64 0 2.50e+00 1.60e-01 4.98e+01 dihedral pdb=" N MET A 629 " pdb=" C MET A 629 " pdb=" CA MET A 629 " pdb=" CB MET A 629 " ideal model delta harmonic sigma weight residual 122.80 138.06 -15.26 0 2.50e+00 1.60e-01 3.73e+01 dihedral pdb=" CA MET A 629 " pdb=" C MET A 629 " pdb=" N GLY A 630 " pdb=" CA GLY A 630 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 9569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 1160 0.148 - 0.297: 28 0.297 - 0.445: 33 0.445 - 0.593: 218 0.593 - 0.742: 147 Chirality restraints: 1586 Sorted by residual: chirality pdb=" CG LEU B 623 " pdb=" CB LEU B 623 " pdb=" CD1 LEU B 623 " pdb=" CD2 LEU B 623 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" CG LEU A 623 " pdb=" CB LEU A 623 " pdb=" CD1 LEU A 623 " pdb=" CD2 LEU A 623 " both_signs ideal model delta sigma weight residual False -2.59 -1.85 -0.74 2.00e-01 2.50e+01 1.37e+01 ... (remaining 1583 not shown) Planarity restraints: 2868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 92 " -0.183 2.00e-02 2.50e+03 6.12e-02 1.50e+02 pdb=" CG TRP A 92 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 92 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP A 92 " 0.020 2.00e-02 2.50e+03 pdb=" NE1 TRP A 92 " 0.039 2.00e-02 2.50e+03 pdb=" CE2 TRP A 92 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP A 92 " 0.044 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 92 " -0.023 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 92 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP A 92 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP A 92 " 0.054 2.00e-02 2.50e+03 pdb=" HE1 TRP A 92 " 0.031 2.00e-02 2.50e+03 pdb=" HE3 TRP A 92 " 0.058 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 92 " -0.085 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 92 " 0.033 2.00e-02 2.50e+03 pdb=" HH2 TRP A 92 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 92 " 0.153 2.00e-02 2.50e+03 5.03e-02 1.01e+02 pdb=" CG TRP B 92 " 0.008 2.00e-02 2.50e+03 pdb=" CD1 TRP B 92 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP B 92 " -0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP B 92 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP B 92 " -0.021 2.00e-02 2.50e+03 pdb=" CE3 TRP B 92 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 92 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 92 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP B 92 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP B 92 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 TRP B 92 " -0.011 2.00e-02 2.50e+03 pdb=" HE3 TRP B 92 " -0.043 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 92 " 0.070 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 92 " -0.018 2.00e-02 2.50e+03 pdb=" HH2 TRP B 92 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 185 " -0.153 9.50e-02 1.11e+02 7.50e-02 7.08e+01 pdb=" NE ARG B 185 " -0.029 2.00e-02 2.50e+03 pdb=" CZ ARG B 185 " -0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG B 185 " -0.060 2.00e-02 2.50e+03 pdb=" NH2 ARG B 185 " -0.014 2.00e-02 2.50e+03 pdb="HH11 ARG B 185 " 0.122 2.00e-02 2.50e+03 pdb="HH12 ARG B 185 " -0.055 2.00e-02 2.50e+03 pdb="HH21 ARG B 185 " 0.049 2.00e-02 2.50e+03 pdb="HH22 ARG B 185 " 0.031 2.00e-02 2.50e+03 ... (remaining 2865 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 704 2.15 - 2.77: 37286 2.77 - 3.38: 56753 3.38 - 3.99: 70376 3.99 - 4.60: 110325 Nonbonded interactions: 275444 Sorted by model distance: nonbonded pdb=" O THR A 263 " pdb=" HG1 THR A 264 " model vdw 1.543 1.850 nonbonded pdb=" O VAL A 449 " pdb=" HG1 THR A 452 " model vdw 1.547 1.850 nonbonded pdb=" O GLU A 352 " pdb=" HG1 THR A 355 " model vdw 1.581 1.850 nonbonded pdb=" O SER B 278 " pdb=" HG SER B 281 " model vdw 1.583 1.850 nonbonded pdb=" HH TYR A 305 " pdb=" OE2 GLU A 673 " model vdw 1.591 1.850 ... (remaining 275439 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' and (resid 16 through 454 or resid 459 through 690)) } 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: 5.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.440 Extract box with map and model: 17.560 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 65.480 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.070 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 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 : 0.029 0.164 10280 Z= 1.853 Angle : 2.072 11.838 13979 Z= 1.395 Chirality : 0.294 0.742 1586 Planarity : 0.010 0.104 1709 Dihedral : 12.649 88.847 3595 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.52 % Favored : 98.40 % Rotamer: Outliers : 0.55 % Allowed : 3.23 % Favored : 96.21 % Cbeta Deviations : 15.76 % Peptide Plane: Cis-proline : 11.11 % 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: -0.52 (0.23), residues: 1187 helix: -0.32 (0.15), residues: 926 sheet: None (None), residues: 0 loop : 0.24 (0.42), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.109 0.011 TRP A 92 HIS 0.013 0.004 HIS A 134 PHE 0.080 0.008 PHE A 599 TYR 0.097 0.011 TYR A 106 ARG 0.016 0.002 ARG B 540 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7049 (t0) REVERT: A 260 ILE cc_start: 0.7258 (mt) cc_final: 0.7042 (mt) REVERT: A 465 GLN cc_start: 0.7415 (mt0) cc_final: 0.6684 (mt0) REVERT: A 468 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7131 (mt-10) REVERT: A 490 ASN cc_start: 0.7660 (m-40) cc_final: 0.7251 (m110) REVERT: A 563 PRO cc_start: 0.7130 (Cg_endo) cc_final: 0.6903 (Cg_exo) REVERT: A 637 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6810 (mm-30) REVERT: B 322 MET cc_start: 0.7012 (tpp) cc_final: 0.6628 (tpp) REVERT: B 438 PHE cc_start: 0.7489 (t80) cc_final: 0.7217 (t80) REVERT: B 671 VAL cc_start: 0.7748 (t) cc_final: 0.7462 (p) REVERT: B 679 LEU cc_start: 0.8030 (mt) cc_final: 0.7808 (mt) outliers start: 6 outliers final: 2 residues processed: 268 average time/residue: 0.5464 time to fit residues: 198.4020 Evaluate side-chains 236 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 233 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain B residue 160 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.8980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 108 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 665 ASN A 690 GLN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10280 Z= 0.287 Angle : 0.584 6.301 13979 Z= 0.319 Chirality : 0.038 0.175 1586 Planarity : 0.004 0.042 1709 Dihedral : 5.643 87.354 1323 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 0.93 % Favored : 98.99 % Rotamer: Outliers : 1.48 % Allowed : 8.68 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.48 (0.24), residues: 1187 helix: 1.20 (0.16), residues: 924 sheet: None (None), residues: 0 loop : 0.53 (0.43), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 271 HIS 0.011 0.002 HIS B 27 PHE 0.022 0.002 PHE B 624 TYR 0.024 0.002 TYR B 294 ARG 0.004 0.001 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 248 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7235 (t0) REVERT: A 465 GLN cc_start: 0.7425 (mt0) cc_final: 0.6762 (mt0) REVERT: A 490 ASN cc_start: 0.7683 (m-40) cc_final: 0.7438 (m-40) REVERT: B 212 MET cc_start: 0.6647 (ptm) cc_final: 0.6311 (ptp) REVERT: B 438 PHE cc_start: 0.7602 (t80) cc_final: 0.7328 (t80) REVERT: B 621 VAL cc_start: 0.7095 (t) cc_final: 0.6848 (m) REVERT: B 629 MET cc_start: 0.7285 (mmm) cc_final: 0.6960 (mmt) REVERT: B 648 SER cc_start: 0.7918 (p) cc_final: 0.7665 (t) outliers start: 16 outliers final: 12 residues processed: 258 average time/residue: 0.5180 time to fit residues: 182.2790 Evaluate side-chains 256 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 243 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASN Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 677 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 9.9990 chunk 33 optimal weight: 0.0870 chunk 90 optimal weight: 2.9990 chunk 74 optimal weight: 0.0060 chunk 30 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 117 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 ASN B 153 ASN B 353 GLN B 665 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10280 Z= 0.219 Angle : 0.525 5.636 13979 Z= 0.286 Chirality : 0.036 0.179 1586 Planarity : 0.004 0.043 1709 Dihedral : 4.562 26.119 1319 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 0.93 % Favored : 98.99 % Rotamer: Outliers : 1.85 % Allowed : 9.88 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.24), residues: 1187 helix: 1.62 (0.16), residues: 924 sheet: None (None), residues: 0 loop : 0.66 (0.43), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.006 0.001 HIS B 27 PHE 0.023 0.001 PHE A 675 TYR 0.021 0.002 TYR B 294 ARG 0.006 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 244 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7383 (t0) REVERT: A 465 GLN cc_start: 0.7407 (mt0) cc_final: 0.6984 (mt0) REVERT: A 490 ASN cc_start: 0.7738 (m-40) cc_final: 0.7491 (m-40) REVERT: A 637 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6484 (tp30) REVERT: A 664 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6902 (mt) REVERT: B 212 MET cc_start: 0.6648 (ptm) cc_final: 0.6351 (ptp) REVERT: B 324 ARG cc_start: 0.7380 (ttt90) cc_final: 0.7168 (ttt90) REVERT: B 326 MET cc_start: 0.6405 (ttm) cc_final: 0.6042 (ttm) REVERT: B 438 PHE cc_start: 0.7612 (t80) cc_final: 0.7341 (t80) REVERT: B 648 SER cc_start: 0.7851 (p) cc_final: 0.7585 (t) outliers start: 20 outliers final: 13 residues processed: 253 average time/residue: 0.5257 time to fit residues: 181.3441 Evaluate side-chains 261 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 246 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 677 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 57 optimal weight: 0.2980 chunk 103 optimal weight: 0.0670 chunk 31 optimal weight: 2.9990 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10280 Z= 0.208 Angle : 0.508 8.372 13979 Z= 0.275 Chirality : 0.035 0.168 1586 Planarity : 0.003 0.036 1709 Dihedral : 4.375 26.033 1319 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.35 % Favored : 98.57 % Rotamer: Outliers : 2.22 % Allowed : 9.14 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.24), residues: 1187 helix: 1.80 (0.16), residues: 935 sheet: None (None), residues: 0 loop : 0.79 (0.45), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.006 0.001 HIS B 27 PHE 0.022 0.001 PHE B 624 TYR 0.016 0.001 TYR B 256 ARG 0.002 0.000 ARG B 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 240 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.7409 (t0) REVERT: A 465 GLN cc_start: 0.7347 (mt0) cc_final: 0.6895 (mt0) REVERT: A 490 ASN cc_start: 0.7760 (m-40) cc_final: 0.7515 (m-40) REVERT: A 500 ASP cc_start: 0.7727 (m-30) cc_final: 0.7385 (m-30) REVERT: A 637 GLU cc_start: 0.7056 (mm-30) cc_final: 0.6685 (tp30) REVERT: B 212 MET cc_start: 0.6705 (ptm) cc_final: 0.6472 (ptp) REVERT: B 258 MET cc_start: 0.7995 (mmp) cc_final: 0.7744 (mmm) REVERT: B 320 ASP cc_start: 0.5948 (m-30) cc_final: 0.5667 (m-30) REVERT: B 324 ARG cc_start: 0.7407 (ttt90) cc_final: 0.7194 (ttt90) REVERT: B 326 MET cc_start: 0.6497 (ttm) cc_final: 0.6096 (ttm) REVERT: B 438 PHE cc_start: 0.7610 (t80) cc_final: 0.7362 (t80) REVERT: B 621 VAL cc_start: 0.6910 (t) cc_final: 0.6703 (m) REVERT: B 629 MET cc_start: 0.7608 (mmm) cc_final: 0.7202 (mmt) REVERT: B 648 SER cc_start: 0.7912 (p) cc_final: 0.7601 (t) outliers start: 24 outliers final: 17 residues processed: 249 average time/residue: 0.5383 time to fit residues: 182.0983 Evaluate side-chains 253 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 235 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 677 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 631 ASN ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 665 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10280 Z= 0.341 Angle : 0.573 6.387 13979 Z= 0.315 Chirality : 0.038 0.179 1586 Planarity : 0.004 0.039 1709 Dihedral : 4.553 26.949 1319 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.27 % Favored : 97.64 % Rotamer: Outliers : 2.49 % Allowed : 9.88 % Favored : 87.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.88 (0.24), residues: 1187 helix: 1.53 (0.16), residues: 943 sheet: None (None), residues: 0 loop : 0.37 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 223 HIS 0.007 0.002 HIS B 27 PHE 0.032 0.002 PHE B 624 TYR 0.020 0.002 TYR B 294 ARG 0.003 0.000 ARG B 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 242 time to evaluate : 1.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8028 (OUTLIER) cc_final: 0.7721 (t0) REVERT: A 465 GLN cc_start: 0.7401 (mt0) cc_final: 0.6987 (mt0) REVERT: A 490 ASN cc_start: 0.7877 (m-40) cc_final: 0.7617 (m-40) REVERT: A 637 GLU cc_start: 0.7144 (mm-30) cc_final: 0.6558 (mm-30) REVERT: B 212 MET cc_start: 0.6939 (ptm) cc_final: 0.6731 (ptp) REVERT: B 258 MET cc_start: 0.7977 (mmp) cc_final: 0.7750 (mmm) REVERT: B 320 ASP cc_start: 0.6278 (m-30) cc_final: 0.5905 (m-30) REVERT: B 324 ARG cc_start: 0.7493 (ttt90) cc_final: 0.7277 (ttt90) REVERT: B 388 PHE cc_start: 0.6899 (t80) cc_final: 0.6481 (t80) REVERT: B 438 PHE cc_start: 0.7676 (t80) cc_final: 0.7438 (t80) REVERT: B 607 ASP cc_start: 0.7620 (t0) cc_final: 0.7373 (t0) REVERT: B 648 SER cc_start: 0.7964 (p) cc_final: 0.7630 (t) outliers start: 27 outliers final: 17 residues processed: 252 average time/residue: 0.5149 time to fit residues: 177.3408 Evaluate side-chains 251 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 233 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 328 GLU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 631 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10280 Z= 0.260 Angle : 0.531 6.968 13979 Z= 0.288 Chirality : 0.036 0.148 1586 Planarity : 0.003 0.038 1709 Dihedral : 4.414 28.904 1319 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.94 % Favored : 97.98 % Rotamer: Outliers : 1.85 % Allowed : 11.82 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.24), residues: 1187 helix: 1.71 (0.16), residues: 941 sheet: None (None), residues: 0 loop : 0.40 (0.43), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 223 HIS 0.006 0.001 HIS B 27 PHE 0.025 0.001 PHE B 624 TYR 0.030 0.002 TYR B 486 ARG 0.003 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 242 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8006 (OUTLIER) cc_final: 0.7649 (t0) REVERT: A 465 GLN cc_start: 0.7378 (mt0) cc_final: 0.6978 (mt0) REVERT: A 490 ASN cc_start: 0.7896 (m-40) cc_final: 0.7573 (m-40) REVERT: B 189 TYR cc_start: 0.8286 (m-80) cc_final: 0.7562 (m-80) REVERT: B 258 MET cc_start: 0.8007 (mmp) cc_final: 0.7773 (mmm) REVERT: B 320 ASP cc_start: 0.6240 (m-30) cc_final: 0.5956 (m-30) REVERT: B 324 ARG cc_start: 0.7482 (ttt90) cc_final: 0.7246 (ttt90) REVERT: B 388 PHE cc_start: 0.6855 (t80) cc_final: 0.6417 (t80) REVERT: B 438 PHE cc_start: 0.7668 (t80) cc_final: 0.7433 (t80) REVERT: B 547 ASN cc_start: 0.6935 (m-40) cc_final: 0.6668 (m-40) REVERT: B 607 ASP cc_start: 0.7613 (t0) cc_final: 0.7402 (t0) REVERT: B 648 SER cc_start: 0.7962 (p) cc_final: 0.7601 (t) outliers start: 20 outliers final: 16 residues processed: 251 average time/residue: 0.5194 time to fit residues: 178.7133 Evaluate side-chains 253 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 236 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 0.5980 chunk 115 optimal weight: 0.3980 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 665 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10280 Z= 0.192 Angle : 0.499 7.207 13979 Z= 0.268 Chirality : 0.035 0.139 1586 Planarity : 0.003 0.039 1709 Dihedral : 4.210 23.735 1319 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.23 % Rotamer: Outliers : 1.66 % Allowed : 12.56 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.24), residues: 1187 helix: 1.99 (0.16), residues: 941 sheet: None (None), residues: 0 loop : 0.53 (0.44), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.008 0.001 HIS B 27 PHE 0.022 0.001 PHE B 624 TYR 0.014 0.001 TYR B 106 ARG 0.002 0.000 ARG A 543 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 240 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8019 (OUTLIER) cc_final: 0.7631 (t0) REVERT: A 465 GLN cc_start: 0.7359 (mt0) cc_final: 0.6972 (mt0) REVERT: A 490 ASN cc_start: 0.8021 (m-40) cc_final: 0.7721 (m-40) REVERT: A 500 ASP cc_start: 0.7686 (m-30) cc_final: 0.7452 (m-30) REVERT: B 189 TYR cc_start: 0.8269 (m-80) cc_final: 0.7666 (m-80) REVERT: B 320 ASP cc_start: 0.6375 (m-30) cc_final: 0.6046 (m-30) REVERT: B 324 ARG cc_start: 0.7479 (ttt90) cc_final: 0.7277 (ttt90) REVERT: B 388 PHE cc_start: 0.6834 (t80) cc_final: 0.6399 (t80) REVERT: B 438 PHE cc_start: 0.7664 (t80) cc_final: 0.7435 (t80) REVERT: B 547 ASN cc_start: 0.7066 (m-40) cc_final: 0.6767 (m-40) REVERT: B 607 ASP cc_start: 0.7622 (t0) cc_final: 0.7386 (t0) REVERT: B 648 SER cc_start: 0.7982 (p) cc_final: 0.7591 (t) outliers start: 18 outliers final: 14 residues processed: 249 average time/residue: 0.5237 time to fit residues: 177.8467 Evaluate side-chains 252 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 237 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 10280 Z= 0.360 Angle : 0.556 6.948 13979 Z= 0.305 Chirality : 0.038 0.141 1586 Planarity : 0.004 0.039 1709 Dihedral : 4.380 25.371 1319 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.19 % Favored : 97.73 % Rotamer: Outliers : 1.85 % Allowed : 13.02 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.24), residues: 1187 helix: 1.67 (0.16), residues: 947 sheet: None (None), residues: 0 loop : 0.10 (0.42), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 223 HIS 0.008 0.002 HIS B 27 PHE 0.020 0.001 PHE B 624 TYR 0.020 0.002 TYR B 294 ARG 0.002 0.000 ARG B 279 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8065 (OUTLIER) cc_final: 0.7710 (t0) REVERT: A 465 GLN cc_start: 0.7362 (mt0) cc_final: 0.7037 (mt0) REVERT: A 490 ASN cc_start: 0.8038 (m-40) cc_final: 0.7722 (m-40) REVERT: A 500 ASP cc_start: 0.7781 (m-30) cc_final: 0.7556 (m-30) REVERT: B 126 ILE cc_start: 0.8726 (tp) cc_final: 0.8469 (tt) REVERT: B 189 TYR cc_start: 0.8307 (m-80) cc_final: 0.7653 (m-80) REVERT: B 320 ASP cc_start: 0.6460 (m-30) cc_final: 0.6138 (m-30) REVERT: B 324 ARG cc_start: 0.7549 (ttt90) cc_final: 0.7335 (ttt90) REVERT: B 388 PHE cc_start: 0.6933 (t80) cc_final: 0.6549 (t80) REVERT: B 547 ASN cc_start: 0.7110 (m-40) cc_final: 0.6832 (m-40) REVERT: B 584 VAL cc_start: 0.8077 (p) cc_final: 0.7619 (t) REVERT: B 607 ASP cc_start: 0.7619 (t0) cc_final: 0.7414 (t0) REVERT: B 648 SER cc_start: 0.7983 (p) cc_final: 0.7598 (t) outliers start: 20 outliers final: 14 residues processed: 245 average time/residue: 0.5253 time to fit residues: 175.6816 Evaluate side-chains 251 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 145 ARG Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 117 ASN Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 46 optimal weight: 0.4980 chunk 84 optimal weight: 0.0570 chunk 33 optimal weight: 0.5980 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 585 GLN B 625 ASN B 665 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10280 Z= 0.214 Angle : 0.503 6.721 13979 Z= 0.271 Chirality : 0.035 0.135 1586 Planarity : 0.003 0.038 1709 Dihedral : 4.177 23.458 1319 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.68 % Favored : 98.23 % Rotamer: Outliers : 1.39 % Allowed : 14.22 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.24), residues: 1187 helix: 1.94 (0.16), residues: 942 sheet: None (None), residues: 0 loop : 0.32 (0.42), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 148 HIS 0.008 0.001 HIS B 27 PHE 0.022 0.001 PHE B 624 TYR 0.021 0.001 TYR B 78 ARG 0.002 0.000 ARG B 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7606 (t0) REVERT: A 465 GLN cc_start: 0.7329 (mt0) cc_final: 0.7013 (mt0) REVERT: A 490 ASN cc_start: 0.8039 (m-40) cc_final: 0.7743 (m-40) REVERT: A 500 ASP cc_start: 0.7762 (m-30) cc_final: 0.7561 (m-30) REVERT: B 126 ILE cc_start: 0.8712 (tp) cc_final: 0.8469 (tt) REVERT: B 189 TYR cc_start: 0.8289 (m-80) cc_final: 0.7616 (m-80) REVERT: B 320 ASP cc_start: 0.6461 (m-30) cc_final: 0.6103 (m-30) REVERT: B 324 ARG cc_start: 0.7536 (ttt90) cc_final: 0.7321 (ttt90) REVERT: B 388 PHE cc_start: 0.6848 (t80) cc_final: 0.6435 (t80) REVERT: B 547 ASN cc_start: 0.7079 (m-40) cc_final: 0.6803 (m-40) REVERT: B 607 ASP cc_start: 0.7613 (t0) cc_final: 0.7403 (t0) REVERT: B 648 SER cc_start: 0.7973 (p) cc_final: 0.7585 (t) outliers start: 15 outliers final: 14 residues processed: 243 average time/residue: 0.5160 time to fit residues: 173.4605 Evaluate side-chains 248 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 233 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 310 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 0.0030 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.5347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10280 Z= 0.309 Angle : 0.542 8.221 13979 Z= 0.294 Chirality : 0.037 0.138 1586 Planarity : 0.003 0.039 1709 Dihedral : 4.247 24.584 1319 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 1.48 % Allowed : 14.40 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.24), residues: 1187 helix: 1.84 (0.16), residues: 940 sheet: None (None), residues: 0 loop : 0.13 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 148 HIS 0.008 0.001 HIS B 27 PHE 0.020 0.001 PHE B 624 TYR 0.020 0.002 TYR B 78 ARG 0.002 0.000 ARG B 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 235 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.8021 (OUTLIER) cc_final: 0.7688 (t0) REVERT: A 465 GLN cc_start: 0.7356 (mt0) cc_final: 0.7053 (mt0) REVERT: A 500 ASP cc_start: 0.7799 (m-30) cc_final: 0.7587 (m-30) REVERT: B 126 ILE cc_start: 0.8718 (tp) cc_final: 0.8492 (tt) REVERT: B 189 TYR cc_start: 0.8315 (m-80) cc_final: 0.7665 (m-80) REVERT: B 320 ASP cc_start: 0.6547 (m-30) cc_final: 0.6204 (m-30) REVERT: B 324 ARG cc_start: 0.7561 (ttt90) cc_final: 0.7337 (ttt90) REVERT: B 388 PHE cc_start: 0.6912 (t80) cc_final: 0.6542 (t80) REVERT: B 547 ASN cc_start: 0.7090 (m-40) cc_final: 0.6847 (m-40) REVERT: B 584 VAL cc_start: 0.8083 (p) cc_final: 0.7574 (t) REVERT: B 648 SER cc_start: 0.7998 (p) cc_final: 0.7604 (t) outliers start: 16 outliers final: 11 residues processed: 242 average time/residue: 0.5153 time to fit residues: 172.1993 Evaluate side-chains 242 residues out of total 1083 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 230 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 659 THR Chi-restraints excluded: chain B residue 664 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 39 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.3980 chunk 5 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 625 ASN B 665 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.181236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.146142 restraints weight = 43971.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.151885 restraints weight = 17402.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.155212 restraints weight = 9998.581| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10280 Z= 0.260 Angle : 0.531 7.392 13979 Z= 0.287 Chirality : 0.036 0.167 1586 Planarity : 0.003 0.037 1709 Dihedral : 4.170 23.577 1319 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.94 % Favored : 97.98 % Rotamer: Outliers : 1.29 % Allowed : 15.33 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.24), residues: 1187 helix: 1.92 (0.16), residues: 940 sheet: None (None), residues: 0 loop : 0.18 (0.42), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 148 HIS 0.008 0.001 HIS B 27 PHE 0.020 0.001 PHE B 624 TYR 0.022 0.001 TYR B 78 ARG 0.002 0.000 ARG B 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5002.71 seconds wall clock time: 89 minutes 30.62 seconds (5370.62 seconds total)