Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 04:51:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/04_2023/8e4y_27898_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/04_2023/8e4y_27898.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/04_2023/8e4y_27898_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/04_2023/8e4y_27898_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/04_2023/8e4y_27898_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/04_2023/8e4y_27898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/04_2023/8e4y_27898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/04_2023/8e4y_27898_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/04_2023/8e4y_27898_neut_updated.pdb" } resolution = 3.4 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= 0.000 sd= 0.002 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 P 4 5.49 5 S 24 5.16 5 C 3410 2.51 5 N 905 2.21 5 O 951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 96": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A GLU 212": "OE1" <-> "OE2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A GLU 311": "OE1" <-> "OE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A GLU 470": "OE1" <-> "OE2" Residue "A GLU 629": "OE1" <-> "OE2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A GLU 750": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5294 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5294 Unusual residues: {'NKO': 1, 'UKL': 1} Classifications: {'peptide': 651, 'undetermined': 2} Link IDs: {'PTRANS': 21, 'TRANS': 629, None: 2} Not linked: pdbres="LEU A 828 " pdbres="UKL A1001 " Not linked: pdbres="UKL A1001 " pdbres="NKO A1002 " Chain breaks: 5 Time building chain proxies: 3.26, per 1000 atoms: 0.62 Number of scatterers: 5294 At special positions: 0 Unit cell: (70.56, 94.08, 97.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 4 15.00 O 951 8.00 N 905 7.00 C 3410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.90 Conformation dependent library (CDL) restraints added in 732.0 milliseconds 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1242 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 4 sheets defined 55.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.713A pdb=" N ARG A 108 " --> pdb=" O TRP A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 104 through 108' Processing helix chain 'A' and resid 110 through 117 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.776A pdb=" N LEU A 150 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 removed outlier: 3.518A pdb=" N LEU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 200 removed outlier: 3.594A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.702A pdb=" N MET A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 246 removed outlier: 3.549A pdb=" N TYR A 236 " --> pdb=" O HIS A 233 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 238 " --> pdb=" O ASP A 235 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A 239 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 240 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 242 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE A 244 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS A 245 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 264 through 271 removed outlier: 3.528A pdb=" N LEU A 271 " --> pdb=" O LEU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 305 Processing helix chain 'A' and resid 332 through 341 removed outlier: 3.603A pdb=" N THR A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 369 Processing helix chain 'A' and resid 380 through 390 removed outlier: 3.580A pdb=" N GLY A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 424 through 432 Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 457 through 479 removed outlier: 4.118A pdb=" N ARG A 461 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 502 through 519 removed outlier: 3.511A pdb=" N VAL A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 519 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 539 removed outlier: 3.761A pdb=" N VAL A 533 " --> pdb=" O SER A 529 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLN A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 539 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 594 removed outlier: 4.050A pdb=" N PHE A 567 " --> pdb=" O VAL A 563 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLU A 568 " --> pdb=" O PRO A 564 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLY A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL A 576 " --> pdb=" O TYR A 572 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N HIS A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL A 579 " --> pdb=" O GLY A 575 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 580 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N MET A 582 " --> pdb=" O HIS A 578 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLU A 583 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR A 591 " --> pdb=" O ALA A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 625 removed outlier: 3.520A pdb=" N TYR A 624 " --> pdb=" O ALA A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 653 Processing helix chain 'A' and resid 712 through 741 removed outlier: 3.897A pdb=" N GLN A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 725 " --> pdb=" O LEU A 721 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 726 " --> pdb=" O GLN A 722 " (cutoff:3.500A) Proline residue: A 727 - end of helix removed outlier: 3.719A pdb=" N TYR A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N HIS A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 765 removed outlier: 3.695A pdb=" N GLN A 753 " --> pdb=" O PRO A 749 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 763 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 774 Processing helix chain 'A' and resid 776 through 789 removed outlier: 3.517A pdb=" N ASP A 788 " --> pdb=" O LYS A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 823 removed outlier: 3.513A pdb=" N GLN A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 88 through 90 removed outlier: 4.881A pdb=" N HIS A 207 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N PHE A 400 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE A 350 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 225 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N VAL A 352 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LEU A 227 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ILE A 354 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 253 through 256 Processing sheet with id= C, first strand: chain 'A' and resid 544 through 548 Processing sheet with id= D, first strand: chain 'A' and resid 656 through 658 221 hydrogen bonds defined for protein. 648 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: 1.41 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 989 1.33 - 1.45: 1266 1.45 - 1.58: 3100 1.58 - 1.70: 6 1.70 - 1.82: 35 Bond restraints: 5396 Sorted by residual: bond pdb=" C49 UKL A1001 " pdb=" C51 UKL A1001 " ideal model delta sigma weight residual 1.278 1.532 -0.254 2.00e-02 2.50e+03 1.61e+02 bond pdb=" C51 UKL A1001 " pdb=" O53 UKL A1001 " ideal model delta sigma weight residual 1.668 1.422 0.246 2.00e-02 2.50e+03 1.52e+02 bond pdb=" C45 UKL A1001 " pdb=" O53 UKL A1001 " ideal model delta sigma weight residual 1.297 1.445 -0.148 2.00e-02 2.50e+03 5.45e+01 bond pdb=" C27 UKL A1001 " pdb=" N26 UKL A1001 " ideal model delta sigma weight residual 1.481 1.334 0.147 2.00e-02 2.50e+03 5.44e+01 bond pdb=" C22 UKL A1001 " pdb=" N21 UKL A1001 " ideal model delta sigma weight residual 1.477 1.331 0.146 2.00e-02 2.50e+03 5.31e+01 ... (remaining 5391 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.74: 136 106.74 - 113.64: 2966 113.64 - 120.53: 2338 120.53 - 127.43: 1826 127.43 - 134.32: 34 Bond angle restraints: 7300 Sorted by residual: angle pdb=" C THR A 562 " pdb=" N VAL A 563 " pdb=" CA VAL A 563 " ideal model delta sigma weight residual 120.24 125.60 -5.36 6.30e-01 2.52e+00 7.24e+01 angle pdb=" C ASN A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta sigma weight residual 119.94 125.68 -5.74 1.11e+00 8.12e-01 2.67e+01 angle pdb=" C LYS A 208 " pdb=" N GLY A 209 " pdb=" CA GLY A 209 " ideal model delta sigma weight residual 120.03 125.49 -5.46 1.12e+00 7.97e-01 2.37e+01 angle pdb=" C ARG A 383 " pdb=" N GLY A 384 " pdb=" CA GLY A 384 " ideal model delta sigma weight residual 120.00 125.12 -5.12 1.10e+00 8.26e-01 2.17e+01 angle pdb=" C THR A 189 " pdb=" N GLY A 190 " pdb=" CA GLY A 190 " ideal model delta sigma weight residual 120.03 125.22 -5.19 1.12e+00 7.97e-01 2.15e+01 ... (remaining 7295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.80: 3148 33.80 - 67.59: 80 67.59 - 101.39: 2 101.39 - 135.19: 1 135.19 - 168.98: 2 Dihedral angle restraints: 3233 sinusoidal: 1324 harmonic: 1909 Sorted by residual: dihedral pdb=" C19 UKL A1001 " pdb=" C20 UKL A1001 " pdb=" N21 UKL A1001 " pdb=" C22 UKL A1001 " ideal model delta sinusoidal sigma weight residual -115.64 53.34 -168.98 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O42 UKL A1001 " pdb=" O39 UKL A1001 " pdb=" P40 UKL A1001 " pdb=" P36 UKL A1001 " ideal model delta sinusoidal sigma weight residual 4.99 -163.26 168.25 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" CA GLU A 794 " pdb=" C GLU A 794 " pdb=" N THR A 795 " pdb=" CA THR A 795 " ideal model delta harmonic sigma weight residual 180.00 158.71 21.29 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 3230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 370 0.061 - 0.122: 347 0.122 - 0.184: 112 0.184 - 0.245: 17 0.245 - 0.306: 3 Chirality restraints: 849 Sorted by residual: chirality pdb=" C49 UKL A1001 " pdb=" C47 UKL A1001 " pdb=" C51 UKL A1001 " pdb=" O64 UKL A1001 " both_signs ideal model delta sigma weight residual False 2.39 2.70 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ARG A 799 " pdb=" N ARG A 799 " pdb=" C ARG A 799 " pdb=" CB ARG A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C29 UKL A1001 " pdb=" C27 UKL A1001 " pdb=" C31 UKL A1001 " pdb=" O70 UKL A1001 " both_signs ideal model delta sigma weight residual False -2.54 -2.26 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 846 not shown) Planarity restraints: 905 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C20 UKL A1001 " -0.199 2.00e-02 2.50e+03 1.65e-01 3.41e+02 pdb=" C22 UKL A1001 " 0.057 2.00e-02 2.50e+03 pdb=" C24 UKL A1001 " -0.144 2.00e-02 2.50e+03 pdb=" N21 UKL A1001 " 0.270 2.00e-02 2.50e+03 pdb=" O23 UKL A1001 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C25 UKL A1001 " -0.070 2.00e-02 2.50e+03 5.77e-02 4.16e+01 pdb=" C27 UKL A1001 " 0.013 2.00e-02 2.50e+03 pdb=" C29 UKL A1001 " -0.051 2.00e-02 2.50e+03 pdb=" N26 UKL A1001 " 0.094 2.00e-02 2.50e+03 pdb=" O28 UKL A1001 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 292 " 0.020 2.00e-02 2.50e+03 1.14e-02 2.62e+00 pdb=" CG TYR A 292 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 292 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 292 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 292 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 292 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 292 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 292 " 0.006 2.00e-02 2.50e+03 ... (remaining 902 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 1580 2.91 - 3.41: 5320 3.41 - 3.90: 8350 3.90 - 4.40: 9019 4.40 - 4.90: 15871 Nonbonded interactions: 40140 Sorted by model distance: nonbonded pdb=" NH1 ARG A 278 " pdb=" O37 UKL A1001 " model vdw 2.412 2.520 nonbonded pdb=" O ILE A 760 " pdb=" OG1 THR A 763 " model vdw 2.443 2.440 nonbonded pdb=" OD2 ASP A 346 " pdb=" OG SER A 405 " model vdw 2.516 2.440 nonbonded pdb=" OE1 GLU A 361 " pdb=" OH TYR A 364 " model vdw 2.524 2.440 nonbonded pdb=" O GLU A 515 " pdb=" NH1 ARG A 519 " model vdw 2.562 2.520 ... (remaining 40135 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 individual isotropic 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: 2.490 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: 13.020 Check model and map are aligned: 0.100 Set scattering table: 0.050 Process input model: 17.520 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 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 : 0.016 0.254 5396 Z= 0.990 Angle : 1.861 12.879 7300 Z= 1.375 Chirality : 0.088 0.306 849 Planarity : 0.006 0.165 905 Dihedral : 15.217 168.982 1991 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 0.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.27), residues: 639 helix: -1.30 (0.23), residues: 356 sheet: -1.33 (0.53), residues: 65 loop : -1.91 (0.36), residues: 218 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.642 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2349 time to fit residues: 21.6409 Evaluate side-chains 37 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 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 95 ASN A 198 ASN A 297 HIS ** A 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN A 714 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7005 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 5396 Z= 0.179 Angle : 0.488 5.185 7300 Z= 0.264 Chirality : 0.038 0.159 849 Planarity : 0.004 0.036 905 Dihedral : 12.935 177.651 745 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.31), residues: 639 helix: 1.06 (0.26), residues: 377 sheet: -0.39 (0.67), residues: 57 loop : -1.56 (0.38), residues: 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.684 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 52 average time/residue: 0.1775 time to fit residues: 12.5108 Evaluate side-chains 44 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0572 time to fit residues: 1.4906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 16 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5396 Z= 0.204 Angle : 0.454 8.199 7300 Z= 0.240 Chirality : 0.038 0.144 849 Planarity : 0.004 0.034 905 Dihedral : 12.570 174.360 745 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.33), residues: 639 helix: 1.63 (0.26), residues: 380 sheet: -0.08 (0.68), residues: 58 loop : -1.40 (0.39), residues: 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.670 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 45 average time/residue: 0.1719 time to fit residues: 10.7396 Evaluate side-chains 39 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0636 time to fit residues: 1.3124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 31 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 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 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 715 GLN A 814 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5396 Z= 0.176 Angle : 0.423 5.534 7300 Z= 0.224 Chirality : 0.037 0.138 849 Planarity : 0.004 0.033 905 Dihedral : 12.278 172.812 745 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.33), residues: 639 helix: 1.91 (0.27), residues: 380 sheet: 0.16 (0.69), residues: 58 loop : -1.35 (0.41), residues: 201 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.722 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.1573 time to fit residues: 9.3822 Evaluate side-chains 36 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.638 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0545 time to fit residues: 1.1231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 0.3980 chunk 21 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 HIS A 814 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5396 Z= 0.159 Angle : 0.411 5.621 7300 Z= 0.216 Chirality : 0.037 0.168 849 Planarity : 0.003 0.032 905 Dihedral : 12.063 172.499 745 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.33), residues: 639 helix: 2.06 (0.27), residues: 375 sheet: 0.78 (0.80), residues: 46 loop : -1.49 (0.38), residues: 218 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.608 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 36 average time/residue: 0.1857 time to fit residues: 9.2685 Evaluate side-chains 32 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0522 time to fit residues: 0.9580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5396 Z= 0.249 Angle : 0.459 6.385 7300 Z= 0.238 Chirality : 0.038 0.167 849 Planarity : 0.004 0.033 905 Dihedral : 12.209 174.697 745 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.33), residues: 639 helix: 1.84 (0.27), residues: 381 sheet: 0.78 (0.80), residues: 46 loop : -1.43 (0.39), residues: 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 32 time to evaluate : 0.594 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.1854 time to fit residues: 9.4917 Evaluate side-chains 35 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0680 time to fit residues: 1.2083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5396 Z= 0.197 Angle : 0.426 5.863 7300 Z= 0.222 Chirality : 0.038 0.157 849 Planarity : 0.004 0.032 905 Dihedral : 12.070 171.949 745 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.33), residues: 639 helix: 1.93 (0.27), residues: 379 sheet: 0.86 (0.81), residues: 46 loop : -1.36 (0.39), residues: 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 33 time to evaluate : 0.665 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1801 time to fit residues: 8.5187 Evaluate side-chains 30 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 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 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 HIS ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 5396 Z= 0.299 Angle : 0.484 6.864 7300 Z= 0.250 Chirality : 0.039 0.168 849 Planarity : 0.004 0.036 905 Dihedral : 12.299 174.965 745 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.33), residues: 639 helix: 1.76 (0.27), residues: 377 sheet: 0.90 (0.83), residues: 46 loop : -1.31 (0.40), residues: 216 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.657 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 32 average time/residue: 0.1758 time to fit residues: 8.1073 Evaluate side-chains 29 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 28 time to evaluate : 0.647 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0530 time to fit residues: 0.9769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.0070 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5396 Z= 0.168 Angle : 0.423 6.012 7300 Z= 0.219 Chirality : 0.037 0.153 849 Planarity : 0.003 0.032 905 Dihedral : 12.106 171.888 745 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.34), residues: 639 helix: 1.96 (0.27), residues: 378 sheet: 1.01 (0.84), residues: 46 loop : -1.30 (0.41), residues: 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.639 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 32 average time/residue: 0.1737 time to fit residues: 8.0593 Evaluate side-chains 31 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 30 time to evaluate : 0.631 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0552 time to fit residues: 0.9587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.0670 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 5396 Z= 0.245 Angle : 0.458 6.648 7300 Z= 0.235 Chirality : 0.038 0.159 849 Planarity : 0.004 0.033 905 Dihedral : 12.188 173.406 745 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.34), residues: 639 helix: 1.86 (0.27), residues: 378 sheet: 1.00 (0.84), residues: 46 loop : -1.30 (0.41), residues: 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1278 Ramachandran restraints generated. 639 Oldfield, 0 Emsley, 639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.664 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.1834 time to fit residues: 8.2322 Evaluate side-chains 30 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 0.681 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 6 optimal weight: 0.0060 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.111316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092157 restraints weight = 7914.221| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.11 r_work: 0.2967 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5396 Z= 0.179 Angle : 0.428 7.611 7300 Z= 0.220 Chirality : 0.037 0.151 849 Planarity : 0.003 0.033 905 Dihedral : 12.086 171.949 745 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.34), residues: 639 helix: 2.01 (0.27), residues: 378 sheet: 1.01 (0.85), residues: 46 loop : -1.30 (0.41), residues: 215 =============================================================================== Job complete usr+sys time: 1413.23 seconds wall clock time: 26 minutes 15.59 seconds (1575.59 seconds total)