Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 09:04:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/04_2023/7n88_24233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/04_2023/7n88_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_24233/04_2023/7n88_24233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/04_2023/7n88_24233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/04_2023/7n88_24233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/04_2023/7n88_24233_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-1.21rc1-4938/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: 5.54, per 1000 atoms: 0.59 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: 3.95 Conformation dependent library (CDL) restraints added in 1.6 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: 1.07 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: 2.83 Time building geometry restraints manager: 4.28 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: 0.730 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: 4.300 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.480 Find NCS groups from input model: 0.360 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: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 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 % 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 *********************** 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 : 1.062 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 0.2662 time to fit residues: 36.7801 Evaluate side-chains 68 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.168 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0930 time to fit residues: 2.1252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 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: 0.6480 ------------------------------------------------------------------------------- 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: 0.7001 moved from start: 0.1324 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= 0.223 Angle : 0.782 12.345 12956 Z= 0.406 Chirality : 0.046 0.296 1383 Planarity : 0.006 0.081 1722 Dihedral : 7.397 51.791 1317 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.56 % Favored : 84.44 % Rotamer Outliers : 2.64 % 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: -5.38 (0.18), residues: 1208 helix: -3.25 (0.25), residues: 229 sheet: -2.69 (0.31), residues: 224 loop : -4.22 (0.17), residues: 755 *********************** 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 133 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 1.178 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 128 average time/residue: 0.2249 time to fit residues: 40.4849 Evaluate side-chains 83 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.125 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0952 time to fit residues: 3.6164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9592 Z= 0.214 Angle : 0.769 15.225 12956 Z= 0.396 Chirality : 0.046 0.281 1383 Planarity : 0.005 0.076 1722 Dihedral : 7.053 51.062 1317 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.74 % Favored : 85.18 % Rotamer Outliers : 3.15 % 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: -4.77 (0.20), residues: 1208 helix: -2.63 (0.28), residues: 231 sheet: -2.47 (0.31), residues: 225 loop : -3.79 (0.18), residues: 752 *********************** 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 125 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 1.153 Fit side-chains outliers start: 31 outliers final: 11 residues processed: 121 average time/residue: 0.1979 time to fit residues: 35.0431 Evaluate side-chains 85 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0896 time to fit residues: 3.3825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 111 optimal weight: 0.6980 chunk 117 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 98 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 ASN ** B 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.115 9592 Z= 0.256 Angle : 0.778 14.580 12956 Z= 0.398 Chirality : 0.046 0.277 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.744 50.794 1317 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.40 % Favored : 84.52 % Rotamer Outliers : 2.95 % 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: -4.53 (0.21), residues: 1208 helix: -2.41 (0.30), residues: 231 sheet: -2.45 (0.31), residues: 245 loop : -3.60 (0.20), residues: 732 *********************** 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 116 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 1.104 Fit side-chains outliers start: 29 outliers final: 13 residues processed: 109 average time/residue: 0.2053 time to fit residues: 33.0388 Evaluate side-chains 86 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0940 time to fit residues: 3.7886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 87 optimal weight: 0.4980 chunk 48 optimal weight: 40.0000 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 617 GLN B 624 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.107 9592 Z= 0.270 Angle : 0.772 16.404 12956 Z= 0.396 Chirality : 0.046 0.270 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.948 59.692 1317 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 15.73 % Favored : 84.19 % Rotamer Outliers : 2.44 % 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: -4.37 (0.21), residues: 1208 helix: -2.29 (0.30), residues: 230 sheet: -2.24 (0.32), residues: 235 loop : -3.52 (0.20), residues: 743 *********************** 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 114 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 90 time to evaluate : 1.133 Fit side-chains outliers start: 24 outliers final: 12 residues processed: 109 average time/residue: 0.2014 time to fit residues: 32.4535 Evaluate side-chains 88 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0944 time to fit residues: 3.6229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.7980 chunk 23 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 30.0000 chunk 61 optimal weight: 0.0470 chunk 113 optimal weight: 0.9990 overall best weight: 0.9682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 9592 Z= 0.225 Angle : 0.744 13.073 12956 Z= 0.380 Chirality : 0.046 0.265 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.489 45.386 1317 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.90 % Favored : 85.02 % Rotamer Outliers : 2.03 % 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: -4.22 (0.21), residues: 1208 helix: -2.18 (0.31), residues: 229 sheet: -2.12 (0.31), residues: 247 loop : -3.44 (0.20), residues: 732 *********************** 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 112 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 1.188 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 8 residues processed: 106 average time/residue: 0.2186 time to fit residues: 33.6246 Evaluate side-chains 88 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 80 time to evaluate : 1.080 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0972 time to fit residues: 3.0008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 117 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 9592 Z= 0.345 Angle : 0.810 14.755 12956 Z= 0.414 Chirality : 0.049 0.268 1383 Planarity : 0.006 0.090 1722 Dihedral : 6.850 46.302 1317 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.14 % Favored : 82.86 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 5.77 % 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: -4.33 (0.21), residues: 1208 helix: -2.24 (0.30), residues: 223 sheet: -2.25 (0.30), residues: 257 loop : -3.50 (0.20), residues: 728 *********************** 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 100 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 1.132 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 93 average time/residue: 0.2268 time to fit residues: 30.2750 Evaluate side-chains 85 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0949 time to fit residues: 3.1196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 74 optimal weight: 0.1980 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 9592 Z= 0.239 Angle : 0.750 14.992 12956 Z= 0.381 Chirality : 0.046 0.257 1383 Planarity : 0.005 0.080 1722 Dihedral : 6.566 46.891 1317 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.40 % Favored : 85.60 % Rotamer Outliers : 1.73 % 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: -4.15 (0.21), residues: 1208 helix: -1.99 (0.32), residues: 224 sheet: -2.21 (0.30), residues: 256 loop : -3.39 (0.20), residues: 728 *********************** 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 106 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 1.160 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 101 average time/residue: 0.2292 time to fit residues: 33.3175 Evaluate side-chains 85 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0920 time to fit residues: 2.7712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9592 Z= 0.254 Angle : 0.770 19.520 12956 Z= 0.390 Chirality : 0.047 0.258 1383 Planarity : 0.005 0.085 1722 Dihedral : 6.559 46.381 1317 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 20.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.65 % Favored : 84.35 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 5.77 % 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: -4.12 (0.21), residues: 1208 helix: -1.92 (0.31), residues: 222 sheet: -2.21 (0.30), residues: 257 loop : -3.37 (0.20), residues: 729 *********************** 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 100 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 1.100 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 95 average time/residue: 0.2329 time to fit residues: 31.6027 Evaluate side-chains 88 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 81 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1004 time to fit residues: 2.8228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0670 chunk 80 optimal weight: 0.3980 chunk 121 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 9592 Z= 0.194 Angle : 0.748 18.188 12956 Z= 0.380 Chirality : 0.045 0.249 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.280 51.682 1317 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer Outliers : 0.31 % 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: -3.85 (0.22), residues: 1208 helix: -1.76 (0.33), residues: 221 sheet: -2.06 (0.31), residues: 256 loop : -3.16 (0.21), residues: 731 ********************** 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 99 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 1.423 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 98 average time/residue: 0.2814 time to fit residues: 40.0011 Evaluate side-chains 86 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 1.251 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1058 time to fit residues: 2.0582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 14 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 99 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 85 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.206239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.171776 restraints weight = 16012.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.169763 restraints weight = 21057.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.171788 restraints weight = 18652.209| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9592 Z= 0.213 Angle : 0.759 18.810 12956 Z= 0.382 Chirality : 0.046 0.254 1383 Planarity : 0.006 0.081 1722 Dihedral : 6.252 50.733 1317 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 3.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.22), residues: 1208 helix: -1.72 (0.33), residues: 221 sheet: -1.84 (0.32), residues: 246 loop : -3.17 (0.21), residues: 741 =============================================================================== Job complete usr+sys time: 1868.54 seconds wall clock time: 35 minutes 0.13 seconds (2100.13 seconds total)