Starting phenix.real_space_refine on Thu Mar 14 17:58:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/03_2024/7n88_24233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/03_2024/7n88_24233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/03_2024/7n88_24233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/03_2024/7n88_24233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/03_2024/7n88_24233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/03_2024/7n88_24233_updated.pdb" } resolution = 3.7 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= 0.002 sd= 0.067 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 Fe 2 7.16 5 S 44 5.16 5 C 5889 2.51 5 N 1650 2.21 5 O 1817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 62": "NH1" <-> "NH2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 434": "NH1" <-> "NH2" Residue "A ARG 526": "NH1" <-> "NH2" Residue "A GLU 555": "OE1" <-> "OE2" Residue "A ARG 557": "NH1" <-> "NH2" Residue "A ARG 600": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A GLU 673": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A GLU 679": "OE1" <-> "OE2" Residue "B ARG 5": "NH1" <-> "NH2" Residue "B ARG 121": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 444": "NH1" <-> "NH2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B GLU 688": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9402 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4164 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 17, 'TRANS': 514} Chain breaks: 4 Chain: "B" Number of atoms: 5238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5238 Unusual residues: {' FE': 2, 'BCT': 2} Inner-chain residues flagged as termini: ['pdbres="LYS B 692 "'] Classifications: {'peptide': 688, 'undetermined': 4} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 652, None: 4} Not linked: pdbres="LYS B 692 " pdbres=" FE B 701 " Not linked: pdbres=" FE B 701 " pdbres=" FE B 702 " Not linked: pdbres=" FE B 702 " pdbres="BCT B 703 " Not linked: pdbres="BCT B 703 " pdbres="BCT B 704 " Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 5, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 63 Time building chain proxies: 5.34, per 1000 atoms: 0.57 Number of scatterers: 9402 At special positions: 0 Unit cell: (92.88, 117.72, 141.48, 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) Fe 2 26.01 S 44 16.00 O 1817 8.00 N 1650 7.00 C 5889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 418 " - pdb=" SG CYS A 419 " distance=2.06 Simple disulfide: pdb=" SG CYS B 10 " - pdb=" SG CYS B 46 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 37 " distance=2.03 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 199 " distance=2.03 Simple disulfide: pdb=" SG CYS B 158 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 171 " - pdb=" SG CYS B 182 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 349 " - pdb=" SG CYS B 381 " distance=2.02 Simple disulfide: pdb=" SG CYS B 359 " - pdb=" SG CYS B 372 " distance=2.02 Simple disulfide: pdb=" SG CYS B 406 " - pdb=" SG CYS B 687 " distance=2.01 Simple disulfide: pdb=" SG CYS B 428 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 460 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 484 " - pdb=" SG CYS B 678 " distance=2.03 Simple disulfide: pdb=" SG CYS B 494 " - pdb=" SG CYS B 508 " distance=2.03 Simple disulfide: pdb=" SG CYS B 505 " - pdb=" SG CYS B 518 " distance=2.03 Simple disulfide: pdb=" SG CYS B 576 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 628 " - pdb=" SG CYS B 633 " distance=2.04 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: 3.49 Conformation dependent library (CDL) restraints added in 1.8 seconds 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 12 sheets defined 17.6% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 116 through 122 removed outlier: 6.344A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 566 through 569 removed outlier: 3.798A pdb=" N ASP A 569 " --> pdb=" O ASN A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 21 through 28 Processing helix chain 'B' and resid 43 through 51 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 127 through 137 Proline residue: B 135 - end of helix Processing helix chain 'B' and resid 169 through 171 No H-bonds generated for 'chain 'B' and resid 169 through 171' Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 195 through 201 removed outlier: 4.834A pdb=" N LEU B 200 " --> pdb=" O ALA B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 245 removed outlier: 5.076A pdb=" N LYS B 244 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 278 Processing helix chain 'B' and resid 317 through 320 No H-bonds generated for 'chain 'B' and resid 317 through 320' Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 352 through 366 Processing helix chain 'B' and resid 378 through 387 removed outlier: 4.147A pdb=" N LYS B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 406 removed outlier: 4.177A pdb=" N CYS B 406 " --> pdb=" O THR B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 430 No H-bonds generated for 'chain 'B' and resid 428 through 430' Processing helix chain 'B' and resid 451 through 454 removed outlier: 3.628A pdb=" N VAL B 454 " --> pdb=" O TRP B 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 454' Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 529 through 537 removed outlier: 3.774A pdb=" N ALA B 537 " --> pdb=" O PHE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 552 removed outlier: 3.676A pdb=" N LEU B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 548 through 552' Processing helix chain 'B' and resid 569 through 571 No H-bonds generated for 'chain 'B' and resid 569 through 571' Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 614 through 617 No H-bonds generated for 'chain 'B' and resid 614 through 617' Processing helix chain 'B' and resid 660 through 662 No H-bonds generated for 'chain 'B' and resid 660 through 662' Processing helix chain 'B' and resid 665 through 677 removed outlier: 3.541A pdb=" N ALA B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 677 " --> pdb=" O THR B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 691 removed outlier: 4.212A pdb=" N ALA B 686 " --> pdb=" O PRO B 682 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG B 691 " --> pdb=" O CYS B 687 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 48 through 52 Processing sheet with id= B, first strand: chain 'A' and resid 230 through 236 removed outlier: 6.599A pdb=" N LEU A 246 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASN A 266 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLY A 244 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR A 268 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU A 242 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 377 through 379 removed outlier: 5.569A pdb=" N LEU A 530 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 701 through 703 removed outlier: 4.204A pdb=" N HIS A 549 " --> pdb=" O ASP A 703 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 554 through 557 Processing sheet with id= F, first strand: chain 'A' and resid 140 through 143 Processing sheet with id= G, first strand: chain 'A' and resid 400 through 406 removed outlier: 5.445A pdb=" N VAL A 415 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR A 404 " --> pdb=" O MET A 413 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET A 413 " --> pdb=" O THR A 404 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 308 through 310 removed outlier: 6.894A pdb=" N VAL B 256 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 95 through 98 Processing sheet with id= J, first strand: chain 'B' and resid 393 through 396 removed outlier: 3.508A pdb=" N LEU B 412 " --> pdb=" O VAL B 600 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER B 602 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 593 through 595 Processing sheet with id= L, first strand: chain 'B' and resid 441 through 443 210 hydrogen bonds defined for protein. 558 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: 2.72 Time building geometry restraints manager: 3.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3175 1.35 - 1.48: 2345 1.48 - 1.60: 4018 1.60 - 1.73: 0 1.73 - 1.86: 54 Bond restraints: 9592 Sorted by residual: bond pdb=" C BCT B 703 " pdb=" O3 BCT B 703 " ideal model delta sigma weight residual 1.389 1.292 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C BCT B 704 " pdb=" O3 BCT B 704 " ideal model delta sigma weight residual 1.389 1.297 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C VAL B 519 " pdb=" N PRO B 520 " ideal model delta sigma weight residual 1.334 1.301 0.032 8.40e-03 1.42e+04 1.48e+01 bond pdb=" CA LEU A 54 " pdb=" CB LEU A 54 " ideal model delta sigma weight residual 1.528 1.438 0.090 2.61e-02 1.47e+03 1.19e+01 bond pdb=" C BCT B 704 " pdb=" O2 BCT B 704 " ideal model delta sigma weight residual 1.241 1.296 -0.055 2.00e-02 2.50e+03 7.51e+00 ... (remaining 9587 not shown) Histogram of bond angle deviations from ideal: 97.64 - 105.34: 176 105.34 - 113.05: 5004 113.05 - 120.76: 4392 120.76 - 128.46: 3325 128.46 - 136.17: 59 Bond angle restraints: 12956 Sorted by residual: angle pdb=" C CYS A 418 " pdb=" N CYS A 419 " pdb=" CA CYS A 419 " ideal model delta sigma weight residual 121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01 angle pdb=" CA CYS B 633 " pdb=" CB CYS B 633 " pdb=" SG CYS B 633 " ideal model delta sigma weight residual 114.40 101.67 12.73 2.30e+00 1.89e-01 3.06e+01 angle pdb=" N ALA B 223 " pdb=" CA ALA B 223 " pdb=" C ALA B 223 " ideal model delta sigma weight residual 114.56 107.95 6.61 1.27e+00 6.20e-01 2.71e+01 angle pdb=" N MET B 27 " pdb=" CA MET B 27 " pdb=" C MET B 27 " ideal model delta sigma weight residual 114.56 108.38 6.18 1.27e+00 6.20e-01 2.37e+01 angle pdb=" N GLY B 622 " pdb=" CA GLY B 622 " pdb=" C GLY B 622 " ideal model delta sigma weight residual 113.18 123.01 -9.83 2.37e+00 1.78e-01 1.72e+01 ... (remaining 12951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 5029 17.75 - 35.51: 631 35.51 - 53.26: 104 53.26 - 71.02: 16 71.02 - 88.77: 11 Dihedral angle restraints: 5791 sinusoidal: 2314 harmonic: 3477 Sorted by residual: dihedral pdb=" CA CYS B 628 " pdb=" C CYS B 628 " pdb=" N PRO B 629 " pdb=" CA PRO B 629 " ideal model delta harmonic sigma weight residual 180.00 124.60 55.40 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CB CYS B 576 " pdb=" SG CYS B 576 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -167.15 81.15 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CA ILE A 68 " pdb=" C ILE A 68 " pdb=" N PRO A 69 " pdb=" CA PRO A 69 " ideal model delta harmonic sigma weight residual -180.00 -138.53 -41.47 0 5.00e+00 4.00e-02 6.88e+01 ... (remaining 5788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1083 0.065 - 0.129: 274 0.129 - 0.194: 25 0.194 - 0.259: 0 0.259 - 0.323: 1 Chirality restraints: 1383 Sorted by residual: chirality pdb=" CB ILE A 672 " pdb=" CA ILE A 672 " pdb=" CG1 ILE A 672 " pdb=" CG2 ILE A 672 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CB ILE A 323 " pdb=" CA ILE A 323 " pdb=" CG1 ILE A 323 " pdb=" CG2 ILE A 323 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.12e-01 chirality pdb=" CA GLN B 14 " pdb=" N GLN B 14 " pdb=" C GLN B 14 " pdb=" CB GLN B 14 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 1380 not shown) Planarity restraints: 1722 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 472 " -0.052 5.00e-02 4.00e+02 7.76e-02 9.64e+00 pdb=" N PRO B 473 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 141 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO B 142 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 436 " 0.037 2.00e-02 2.50e+03 2.04e-02 8.34e+00 pdb=" CG TYR B 436 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 436 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR B 436 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 436 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 436 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 436 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 436 " 0.015 2.00e-02 2.50e+03 ... (remaining 1719 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 61 2.32 - 2.97: 5409 2.97 - 3.61: 13989 3.61 - 4.26: 21470 4.26 - 4.90: 35224 Nonbonded interactions: 76153 Sorted by model distance: nonbonded pdb="FE FE B 701 " pdb=" O2 BCT B 703 " model vdw 1.680 2.260 nonbonded pdb=" OH TYR B 436 " pdb="FE FE B 701 " model vdw 1.749 2.260 nonbonded pdb=" OD2 ASP B 61 " pdb=" NE2 HIS B 254 " model vdw 1.762 2.520 nonbonded pdb="FE FE B 702 " pdb=" O3 BCT B 704 " model vdw 1.862 2.260 nonbonded pdb=" OD1 ASP B 396 " pdb="FE FE B 701 " model vdw 1.878 2.260 ... (remaining 76148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.400 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 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 : 0.008 0.097 9592 Z= 0.496 Angle : 1.038 15.460 12956 Z= 0.574 Chirality : 0.054 0.323 1383 Planarity : 0.006 0.078 1722 Dihedral : 15.397 88.771 3518 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 28.91 Ramachandran Plot: Outliers : 0.25 % Allowed : 21.44 % Favored : 78.31 % Rotamer: Outliers : 0.81 % Allowed : 9.36 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % 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: -6.39 (0.16), residues: 1208 helix: -4.23 (0.19), residues: 227 sheet: -3.16 (0.29), residues: 212 loop : -4.90 (0.14), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 183 HIS 0.014 0.002 HIS B 598 PHE 0.025 0.003 PHE B 326 TYR 0.040 0.003 TYR B 436 ARG 0.012 0.001 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 117 LYS cc_start: 0.6876 (ttmt) cc_final: 0.6559 (mmtp) REVERT: B 395 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.6012 (pp) outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 0.2517 time to fit residues: 34.4581 Evaluate side-chains 70 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 66 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 95 optimal weight: 0.0470 chunk 37 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 overall best weight: 0.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN B 117 HIS B 330 GLN ** B 598 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9592 Z= 0.227 Angle : 0.780 12.244 12956 Z= 0.405 Chirality : 0.046 0.293 1383 Planarity : 0.006 0.081 1722 Dihedral : 7.657 52.004 1325 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.81 % Favored : 84.19 % Rotamer: Outliers : 2.85 % Allowed : 14.85 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % 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: -5.35 (0.18), residues: 1208 helix: -3.24 (0.25), residues: 229 sheet: -2.55 (0.32), residues: 208 loop : -4.23 (0.17), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 139 HIS 0.018 0.001 HIS B 598 PHE 0.016 0.002 PHE B 301 TYR 0.021 0.002 TYR A 251 ARG 0.009 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.063 Fit side-chains REVERT: B 27 MET cc_start: 0.7072 (tpp) cc_final: 0.6651 (mtt) REVERT: B 67 GLU cc_start: 0.5852 (OUTLIER) cc_final: 0.4442 (mp0) REVERT: B 170 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6572 (tt) REVERT: B 395 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5416 (pp) REVERT: B 648 THR cc_start: 0.8168 (m) cc_final: 0.7919 (p) outliers start: 28 outliers final: 14 residues processed: 132 average time/residue: 0.2248 time to fit residues: 41.4338 Evaluate side-chains 91 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 74 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 0.6980 chunk 75 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 89 optimal weight: 0.0670 chunk 109 optimal weight: 3.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 9592 Z= 0.210 Angle : 0.755 15.071 12956 Z= 0.390 Chirality : 0.045 0.277 1383 Planarity : 0.005 0.077 1722 Dihedral : 7.325 50.781 1325 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.90 % Favored : 85.10 % Rotamer: Outliers : 4.27 % Allowed : 17.50 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % 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: -4.67 (0.20), residues: 1208 helix: -2.55 (0.29), residues: 231 sheet: -2.37 (0.32), residues: 220 loop : -3.74 (0.18), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 563 HIS 0.011 0.001 HIS B 598 PHE 0.012 0.001 PHE A 421 TYR 0.021 0.002 TYR B 527 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 99 time to evaluate : 1.049 Fit side-chains REVERT: A 205 TYR cc_start: 0.6996 (m-80) cc_final: 0.6701 (m-80) REVERT: B 27 MET cc_start: 0.6974 (tpp) cc_final: 0.6645 (mtt) REVERT: B 37 CYS cc_start: 0.6225 (OUTLIER) cc_final: 0.5867 (m) REVERT: B 64 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8273 (m-10) REVERT: B 67 GLU cc_start: 0.5835 (OUTLIER) cc_final: 0.4461 (mp0) REVERT: B 170 LEU cc_start: 0.6233 (OUTLIER) cc_final: 0.5711 (tt) REVERT: B 171 CYS cc_start: 0.3751 (OUTLIER) cc_final: 0.3410 (p) REVERT: B 395 LEU cc_start: 0.6146 (OUTLIER) cc_final: 0.5516 (pp) REVERT: B 633 CYS cc_start: 0.6195 (m) cc_final: 0.5494 (p) REVERT: B 634 LEU cc_start: 0.4797 (OUTLIER) cc_final: 0.4532 (pp) outliers start: 42 outliers final: 20 residues processed: 132 average time/residue: 0.1847 time to fit residues: 35.8269 Evaluate side-chains 104 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 77 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 64 PHE Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 171 CYS Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.1980 chunk 57 optimal weight: 0.1980 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 98 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9592 Z= 0.210 Angle : 0.728 11.037 12956 Z= 0.374 Chirality : 0.045 0.273 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.953 49.713 1325 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.82 % Favored : 86.09 % Rotamer: Outliers : 4.98 % Allowed : 18.62 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % 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: -4.39 (0.21), residues: 1208 helix: -2.32 (0.30), residues: 230 sheet: -2.38 (0.31), residues: 245 loop : -3.48 (0.20), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 563 HIS 0.007 0.001 HIS B 598 PHE 0.036 0.001 PHE B 644 TYR 0.023 0.002 TYR B 527 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 90 time to evaluate : 1.040 Fit side-chains REVERT: A 205 TYR cc_start: 0.7001 (m-80) cc_final: 0.6693 (m-80) REVERT: B 27 MET cc_start: 0.6830 (tpp) cc_final: 0.6472 (mtt) REVERT: B 37 CYS cc_start: 0.6189 (OUTLIER) cc_final: 0.5790 (m) REVERT: B 67 GLU cc_start: 0.5827 (OUTLIER) cc_final: 0.4411 (mp0) REVERT: B 395 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5727 (pp) REVERT: B 412 LEU cc_start: 0.5525 (OUTLIER) cc_final: 0.5287 (mm) REVERT: B 617 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8576 (pt0) REVERT: B 633 CYS cc_start: 0.6031 (m) cc_final: 0.5457 (p) REVERT: B 634 LEU cc_start: 0.4600 (OUTLIER) cc_final: 0.4314 (pp) outliers start: 49 outliers final: 26 residues processed: 132 average time/residue: 0.1881 time to fit residues: 36.2576 Evaluate side-chains 108 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 76 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.1980 chunk 48 optimal weight: 30.0000 chunk 100 optimal weight: 2.9990 chunk 81 optimal weight: 0.0870 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 105 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 516 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9592 Z= 0.195 Angle : 0.699 10.648 12956 Z= 0.358 Chirality : 0.044 0.264 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.736 49.464 1325 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 18.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 4.68 % Allowed : 19.53 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % 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: -4.05 (0.22), residues: 1208 helix: -1.97 (0.32), residues: 228 sheet: -2.24 (0.32), residues: 236 loop : -3.25 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 563 HIS 0.006 0.001 HIS B 598 PHE 0.024 0.001 PHE B 644 TYR 0.026 0.002 TYR B 527 ARG 0.004 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 92 time to evaluate : 1.086 Fit side-chains REVERT: B 27 MET cc_start: 0.6779 (tpp) cc_final: 0.6378 (mtt) REVERT: B 67 GLU cc_start: 0.5723 (OUTLIER) cc_final: 0.4352 (mp0) REVERT: B 395 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5648 (pp) REVERT: B 617 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8319 (pt0) REVERT: B 633 CYS cc_start: 0.5852 (m) cc_final: 0.5415 (p) REVERT: B 634 LEU cc_start: 0.4671 (OUTLIER) cc_final: 0.4344 (pp) outliers start: 46 outliers final: 29 residues processed: 130 average time/residue: 0.1921 time to fit residues: 36.6772 Evaluate side-chains 118 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 85 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 61 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 9592 Z= 0.240 Angle : 0.742 20.648 12956 Z= 0.377 Chirality : 0.045 0.265 1383 Planarity : 0.005 0.080 1722 Dihedral : 7.114 82.718 1325 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 5.09 % Allowed : 20.04 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.97 (0.22), residues: 1208 helix: -1.91 (0.32), residues: 225 sheet: -2.10 (0.31), residues: 247 loop : -3.22 (0.20), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 563 HIS 0.005 0.001 HIS B 598 PHE 0.026 0.002 PHE A 237 TYR 0.028 0.002 TYR B 527 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 89 time to evaluate : 0.948 Fit side-chains REVERT: A 133 TYR cc_start: 0.7768 (p90) cc_final: 0.7513 (p90) REVERT: B 27 MET cc_start: 0.6836 (tpp) cc_final: 0.6416 (mtt) REVERT: B 67 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.4399 (mp0) REVERT: B 395 LEU cc_start: 0.6215 (OUTLIER) cc_final: 0.5812 (pp) REVERT: B 617 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8404 (pt0) REVERT: B 633 CYS cc_start: 0.5935 (m) cc_final: 0.5501 (p) REVERT: B 634 LEU cc_start: 0.4716 (OUTLIER) cc_final: 0.4391 (pp) outliers start: 50 outliers final: 34 residues processed: 133 average time/residue: 0.1890 time to fit residues: 36.8927 Evaluate side-chains 116 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 78 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.0000 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9592 Z= 0.224 Angle : 0.713 13.023 12956 Z= 0.363 Chirality : 0.045 0.260 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.912 68.187 1325 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 4.98 % Allowed : 21.26 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.22), residues: 1208 helix: -1.82 (0.32), residues: 224 sheet: -2.00 (0.32), residues: 239 loop : -3.19 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 563 HIS 0.003 0.001 HIS A 229 PHE 0.034 0.002 PHE A 237 TYR 0.033 0.002 TYR B 527 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 84 time to evaluate : 1.101 Fit side-chains REVERT: A 97 GLN cc_start: 0.7471 (tp40) cc_final: 0.7270 (tp-100) REVERT: A 133 TYR cc_start: 0.7753 (p90) cc_final: 0.7500 (p90) REVERT: B 27 MET cc_start: 0.6713 (tpp) cc_final: 0.6306 (mtt) REVERT: B 67 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.4465 (mp0) REVERT: B 395 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5706 (pp) REVERT: B 617 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: B 633 CYS cc_start: 0.5961 (m) cc_final: 0.5488 (p) REVERT: B 634 LEU cc_start: 0.4755 (OUTLIER) cc_final: 0.4468 (pp) outliers start: 49 outliers final: 37 residues processed: 128 average time/residue: 0.1952 time to fit residues: 36.9198 Evaluate side-chains 119 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 78 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 HIS B 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9592 Z= 0.206 Angle : 0.707 11.887 12956 Z= 0.359 Chirality : 0.044 0.257 1383 Planarity : 0.005 0.080 1722 Dihedral : 6.670 52.575 1325 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 5.09 % Allowed : 21.67 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.22), residues: 1208 helix: -1.67 (0.33), residues: 224 sheet: -1.97 (0.32), residues: 239 loop : -3.13 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 563 HIS 0.002 0.001 HIS A 229 PHE 0.018 0.001 PHE A 237 TYR 0.035 0.002 TYR B 527 ARG 0.002 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 88 time to evaluate : 0.896 Fit side-chains REVERT: A 97 GLN cc_start: 0.7493 (tp40) cc_final: 0.7292 (tp-100) REVERT: A 133 TYR cc_start: 0.7784 (p90) cc_final: 0.7526 (p90) REVERT: B 21 PHE cc_start: 0.7045 (m-80) cc_final: 0.6775 (m-80) REVERT: B 67 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.4354 (mp0) REVERT: B 395 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5712 (pp) REVERT: B 547 LYS cc_start: 0.7938 (ttpt) cc_final: 0.7666 (ttmt) REVERT: B 563 TRP cc_start: 0.6772 (p-90) cc_final: 0.6568 (p-90) REVERT: B 597 ASN cc_start: 0.6545 (OUTLIER) cc_final: 0.6251 (p0) REVERT: B 617 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8341 (pt0) REVERT: B 633 CYS cc_start: 0.5934 (m) cc_final: 0.5537 (p) REVERT: B 634 LEU cc_start: 0.4775 (OUTLIER) cc_final: 0.4464 (pp) outliers start: 50 outliers final: 39 residues processed: 132 average time/residue: 0.1880 time to fit residues: 36.4881 Evaluate side-chains 123 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 79 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 298 PHE Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.0770 chunk 99 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 597 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 9592 Z= 0.197 Angle : 0.705 14.104 12956 Z= 0.357 Chirality : 0.044 0.253 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.476 49.794 1325 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer: Outliers : 5.19 % Allowed : 21.67 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.75 (0.22), residues: 1208 helix: -1.61 (0.33), residues: 224 sheet: -1.96 (0.32), residues: 239 loop : -3.12 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 563 HIS 0.011 0.001 HIS B 598 PHE 0.025 0.001 PHE A 237 TYR 0.037 0.002 TYR B 527 ARG 0.003 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 83 time to evaluate : 1.325 Fit side-chains REVERT: A 133 TYR cc_start: 0.7725 (p90) cc_final: 0.7509 (p90) REVERT: B 21 PHE cc_start: 0.7039 (m-80) cc_final: 0.6793 (m-80) REVERT: B 67 GLU cc_start: 0.5735 (OUTLIER) cc_final: 0.4299 (mp0) REVERT: B 395 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5707 (pp) REVERT: B 597 ASN cc_start: 0.6512 (OUTLIER) cc_final: 0.6217 (p0) REVERT: B 617 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8126 (pt0) REVERT: B 633 CYS cc_start: 0.5900 (m) cc_final: 0.5488 (p) REVERT: B 634 LEU cc_start: 0.4577 (OUTLIER) cc_final: 0.4295 (pp) outliers start: 51 outliers final: 38 residues processed: 126 average time/residue: 0.1885 time to fit residues: 34.9619 Evaluate side-chains 124 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 81 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain B residue 687 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 0.0270 chunk 121 optimal weight: 0.7980 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 597 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9592 Z= 0.195 Angle : 0.711 13.834 12956 Z= 0.358 Chirality : 0.044 0.254 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.400 49.432 1325 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.08 % Favored : 86.92 % Rotamer: Outliers : 4.68 % Allowed : 22.18 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.22), residues: 1208 helix: -1.52 (0.33), residues: 224 sheet: -1.98 (0.32), residues: 247 loop : -3.07 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 563 HIS 0.004 0.001 HIS B 598 PHE 0.025 0.001 PHE A 237 TYR 0.035 0.002 TYR B 527 ARG 0.003 0.000 ARG B 211 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2416 Ramachandran restraints generated. 1208 Oldfield, 0 Emsley, 1208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 83 time to evaluate : 1.045 Fit side-chains REVERT: A 133 TYR cc_start: 0.7736 (p90) cc_final: 0.7518 (p90) REVERT: A 187 THR cc_start: 0.8952 (OUTLIER) cc_final: 0.7786 (t) REVERT: A 413 MET cc_start: 0.7091 (tmm) cc_final: 0.6589 (tmm) REVERT: B 21 PHE cc_start: 0.7069 (m-80) cc_final: 0.6853 (m-80) REVERT: B 67 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.4280 (mp0) REVERT: B 395 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5740 (pp) REVERT: B 597 ASN cc_start: 0.6636 (OUTLIER) cc_final: 0.6379 (p0) REVERT: B 617 GLN cc_start: 0.8467 (OUTLIER) cc_final: 0.8035 (pt0) REVERT: B 633 CYS cc_start: 0.5648 (m) cc_final: 0.5371 (p) REVERT: B 634 LEU cc_start: 0.4591 (OUTLIER) cc_final: 0.4210 (pp) outliers start: 46 outliers final: 38 residues processed: 122 average time/residue: 0.2099 time to fit residues: 37.1641 Evaluate side-chains 123 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 79 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 383 PHE Chi-restraints excluded: chain A residue 405 ILE Chi-restraints excluded: chain A residue 418 CYS Chi-restraints excluded: chain B residue 67 GLU Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 182 CYS Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 445 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 484 CYS Chi-restraints excluded: chain B residue 543 VAL Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 605 ASP Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 616 HIS Chi-restraints excluded: chain B residue 617 GLN Chi-restraints excluded: chain B residue 634 LEU Chi-restraints excluded: chain B residue 646 ASP Chi-restraints excluded: chain B residue 654 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 99 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 597 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.204222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.172558 restraints weight = 15828.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.169212 restraints weight = 20764.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.171291 restraints weight = 20564.091| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.3356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9592 Z= 0.217 Angle : 0.713 13.550 12956 Z= 0.360 Chirality : 0.045 0.254 1383 Planarity : 0.005 0.080 1722 Dihedral : 6.431 48.849 1325 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 17.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer: Outliers : 5.09 % Allowed : 21.77 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.22), residues: 1208 helix: -1.50 (0.33), residues: 224 sheet: -1.97 (0.32), residues: 247 loop : -3.06 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 563 HIS 0.008 0.001 HIS B 598 PHE 0.025 0.001 PHE A 237 TYR 0.034 0.002 TYR B 527 ARG 0.003 0.000 ARG B 211 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1931.78 seconds wall clock time: 35 minutes 47.78 seconds (2147.78 seconds total)