Starting phenix.real_space_refine (version: dev) on Mon Dec 12 06:50:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/12_2022/7n88_24233_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/12_2022/7n88_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_24233/12_2022/7n88_24233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/12_2022/7n88_24233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/12_2022/7n88_24233_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n88_24233/12_2022/7n88_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 Convert atoms to be neutral 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-4807/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: 5.75, per 1000 atoms: 0.61 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: 3.90 Conformation dependent library (CDL) restraints added in 1.5 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: 1.15 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: 2.62 Time building geometry restraints manager: 4.21 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 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. 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: 0.010 Normalize map: mean=0, sd=1: 0.950 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: 4.820 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 27.810 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 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 : 28.96 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 : 1.136 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 101 average time/residue: 0.2435 time to fit residues: 33.9727 Evaluate side-chains 68 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 1.152 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0923 time to fit residues: 2.0826 ------------------------------------------------------------------------------- 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: 0.7089 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 : 1.126 Fit side-chains outliers start: 26 outliers final: 12 residues processed: 128 average time/residue: 0.2312 time to fit residues: 42.2019 Evaluate side-chains 83 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 71 time to evaluate : 1.266 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0984 time to fit residues: 3.8561 ------------------------------------------------------------------------------- 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: 0.1980 chunk 92 optimal weight: 0.5980 chunk 75 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.7037 moved from start: 0.2046 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= 0.205 Angle : 0.769 16.886 12956 Z= 0.396 Chirality : 0.046 0.278 1383 Planarity : 0.005 0.075 1722 Dihedral : 6.993 50.879 1317 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 14.40 % Favored : 85.51 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.09 % 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: -4.69 (0.20), residues: 1208 helix: -2.58 (0.29), residues: 231 sheet: -2.38 (0.32), residues: 220 loop : -3.75 (0.18), residues: 757 *********************** 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 123 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 95 time to evaluate : 1.143 Fit side-chains outliers start: 28 outliers final: 10 residues processed: 119 average time/residue: 0.1888 time to fit residues: 33.3102 Evaluate side-chains 84 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 74 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0876 time to fit residues: 3.1818 ------------------------------------------------------------------------------- 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: 0.9980 chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 30.0000 chunk 74 optimal weight: 6.9990 chunk 111 optimal weight: 0.1980 chunk 117 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.7083 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.112 9592 Z= 0.257 Angle : 0.781 16.164 12956 Z= 0.399 Chirality : 0.047 0.275 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.754 49.721 1317 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.23 % Favored : 84.77 % Rotamer Outliers : 3.46 % 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: -4.51 (0.21), residues: 1208 helix: -2.41 (0.29), residues: 231 sheet: -2.42 (0.31), residues: 245 loop : -3.58 (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 123 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 89 time to evaluate : 1.192 Fit side-chains outliers start: 34 outliers final: 15 residues processed: 116 average time/residue: 0.1979 time to fit residues: 34.0140 Evaluate side-chains 92 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0893 time to fit residues: 4.1129 ------------------------------------------------------------------------------- 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: 0.9980 chunk 1 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 81 optimal weight: 0.0970 chunk 0 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 39 optimal weight: 30.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- 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: 0.7014 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.104 9592 Z= 0.220 Angle : 0.746 17.628 12956 Z= 0.380 Chirality : 0.044 0.264 1383 Planarity : 0.005 0.078 1722 Dihedral : 6.722 64.400 1317 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.49 % Favored : 86.42 % Rotamer Outliers : 2.34 % 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: -4.18 (0.21), residues: 1208 helix: -2.12 (0.31), residues: 224 sheet: -2.33 (0.30), residues: 252 loop : -3.32 (0.20), residues: 732 *********************** 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 115 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 1.112 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 7 residues processed: 111 average time/residue: 0.1995 time to fit residues: 32.4700 Evaluate side-chains 91 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 1.191 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0896 time to fit residues: 2.7900 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 118 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 30.0000 chunk 61 optimal weight: 0.0030 chunk 113 optimal weight: 0.5980 overall best weight: 0.6930 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 9592 Z= 0.201 Angle : 0.723 13.461 12956 Z= 0.369 Chirality : 0.045 0.262 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.194 41.044 1317 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.49 % Favored : 86.42 % Rotamer Outliers : 1.53 % 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: -3.98 (0.22), residues: 1208 helix: -1.88 (0.32), residues: 226 sheet: -2.05 (0.31), residues: 249 loop : -3.28 (0.20), residues: 733 *********************** 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 111 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 96 time to evaluate : 1.019 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 107 average time/residue: 0.2120 time to fit residues: 32.8023 Evaluate side-chains 91 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1058 time to fit residues: 2.7718 ------------------------------------------------------------------------------- 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: 7.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9592 Z= 0.241 Angle : 0.735 14.954 12956 Z= 0.374 Chirality : 0.046 0.261 1383 Planarity : 0.005 0.081 1722 Dihedral : 6.285 43.199 1317 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.24 % Favored : 85.76 % Rotamer Outliers : 1.83 % 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: -4.06 (0.22), residues: 1208 helix: -2.09 (0.31), residues: 232 sheet: -2.00 (0.31), residues: 249 loop : -3.33 (0.20), residues: 727 *********************** 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 111 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.049 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 8 residues processed: 107 average time/residue: 0.2208 time to fit residues: 34.1026 Evaluate side-chains 90 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0974 time to fit residues: 3.0664 ------------------------------------------------------------------------------- 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: 20.0000 chunk 70 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 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: 3.9990 chunk 10 optimal weight: 0.7980 chunk 92 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 9592 Z= 0.203 Angle : 0.730 17.210 12956 Z= 0.369 Chirality : 0.045 0.255 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.155 43.339 1317 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer Outliers : 1.42 % 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: -3.86 (0.22), residues: 1208 helix: -1.83 (0.32), residues: 226 sheet: -1.97 (0.31), residues: 257 loop : -3.19 (0.21), residues: 725 *********************** 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 107 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 1.030 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 105 average time/residue: 0.2229 time to fit residues: 33.6573 Evaluate side-chains 87 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 83 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0907 time to fit residues: 2.2294 ------------------------------------------------------------------------------- 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: 3.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 86 optimal weight: 0.0770 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 71 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 9592 Z= 0.205 Angle : 0.751 19.194 12956 Z= 0.378 Chirality : 0.046 0.255 1383 Planarity : 0.005 0.080 1722 Dihedral : 6.153 49.143 1317 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 18.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.07 % Favored : 85.93 % Rotamer Outliers : 1.42 % 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: -3.80 (0.22), residues: 1208 helix: -1.72 (0.32), residues: 225 sheet: -1.97 (0.31), residues: 257 loop : -3.16 (0.21), residues: 726 *********************** 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 105 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 1.204 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 101 average time/residue: 0.2166 time to fit residues: 31.7000 Evaluate side-chains 90 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0934 time to fit residues: 2.7738 ------------------------------------------------------------------------------- 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: 0.8980 chunk 54 optimal weight: 7.9990 chunk 80 optimal weight: 0.0060 chunk 121 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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: 0.6948 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 9592 Z= 0.189 Angle : 0.736 17.235 12956 Z= 0.369 Chirality : 0.045 0.251 1383 Planarity : 0.005 0.079 1722 Dihedral : 6.062 52.772 1317 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.16 % Favored : 86.84 % Rotamer Outliers : 0.20 % 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: -3.69 (0.22), residues: 1208 helix: -1.67 (0.33), residues: 231 sheet: -1.89 (0.31), residues: 256 loop : -3.08 (0.21), residues: 721 ********************** 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 91 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 89 time to evaluate : 1.142 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 90 average time/residue: 0.2331 time to fit residues: 30.4009 Evaluate side-chains 82 residues out of total 1006 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0884 time to fit residues: 1.9460 ------------------------------------------------------------------------------- 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: 2.9990 chunk 14 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.207797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.174064 restraints weight = 16092.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.172055 restraints weight = 19841.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.174245 restraints weight = 19499.712| |-----------------------------------------------------------------------------| r_work (final): 0.4256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3708 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= 0.205 Angle : 0.730 17.671 12956 Z= 0.368 Chirality : 0.045 0.255 1383 Planarity : 0.005 0.080 1722 Dihedral : 6.035 51.360 1317 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.66 % Favored : 86.34 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.92 % Cis-general : 0.00 % Twisted Proline : 1.92 % 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: -3.67 (0.22), residues: 1208 helix: -1.67 (0.33), residues: 231 sheet: -1.91 (0.31), residues: 261 loop : -3.05 (0.21), residues: 716 =============================================================================== Job complete usr+sys time: 1840.43 seconds wall clock time: 34 minutes 33.22 seconds (2073.22 seconds total)