Starting phenix.real_space_refine on Mon Nov 13 21:23:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/11_2023/8e4y_27898_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/11_2023/8e4y_27898.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/11_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_27898/11_2023/8e4y_27898_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/11_2023/8e4y_27898_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/11_2023/8e4y_27898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/11_2023/8e4y_27898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/11_2023/8e4y_27898_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/11_2023/8e4y_27898_neut_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 3.37, per 1000 atoms: 0.64 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: 1.93 Conformation dependent library (CDL) restraints added in 917.4 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: 1.29 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: 1.37 Time building geometry restraints manager: 2.10 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: 3150 33.80 - 67.59: 85 67.59 - 101.39: 3 101.39 - 135.19: 1 135.19 - 168.98: 3 Dihedral angle restraints: 3242 sinusoidal: 1333 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=" C47 UKL A1001 " pdb=" C44 UKL A1001 " pdb=" C45 UKL A1001 " pdb=" O43 UKL A1001 " ideal model delta sinusoidal sigma weight residual 115.78 -37.41 153.19 1 3.00e+01 1.11e-03 2.02e+01 ... (remaining 3239 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: 2.350 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: 12.130 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.440 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.100 ------------------------------------------------------------------------------- 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 : 15.843 168.982 2000 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 % Allowed : 5.01 % Favored : 94.99 % 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 : 0.639 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2529 time to fit residues: 23.4107 Evaluate side-chains 37 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.575 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8059 ------------------------------------------------------------------------------- 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: 0.7004 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5396 Z= 0.181 Angle : 0.489 5.214 7300 Z= 0.264 Chirality : 0.038 0.159 849 Planarity : 0.004 0.036 905 Dihedral : 14.551 177.607 754 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.07 % Allowed : 7.60 % Favored : 90.33 % 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: 0.14 (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 : 0.612 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 52 average time/residue: 0.1801 time to fit residues: 12.6964 Evaluate side-chains 44 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 38 time to evaluate : 0.607 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0543 time to fit residues: 1.4062 ------------------------------------------------------------------------------- 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: 0.7980 chunk 18 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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** A 715 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5396 Z= 0.200 Angle : 0.444 4.684 7300 Z= 0.238 Chirality : 0.038 0.144 849 Planarity : 0.004 0.035 905 Dihedral : 14.115 174.337 754 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.55 % Allowed : 8.81 % Favored : 89.64 % 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: 0.84 (0.33), residues: 639 helix: 1.65 (0.26), residues: 380 sheet: -0.06 (0.69), 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 47 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.630 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 46 average time/residue: 0.1730 time to fit residues: 11.0680 Evaluate side-chains 37 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.597 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0533 time to fit residues: 1.2274 ------------------------------------------------------------------------------- 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: 1.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 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 814 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5396 Z= 0.202 Angle : 0.434 4.630 7300 Z= 0.230 Chirality : 0.038 0.139 849 Planarity : 0.004 0.033 905 Dihedral : 13.836 173.874 754 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.04 % Allowed : 9.67 % Favored : 89.29 % 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: 1.10 (0.33), residues: 639 helix: 1.84 (0.26), residues: 381 sheet: 0.14 (0.68), residues: 58 loop : -1.31 (0.41), residues: 200 *********************** 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: 6 poor density : 35 time to evaluate : 0.684 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 0.1831 time to fit residues: 10.3271 Evaluate side-chains 35 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 32 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0562 time to fit residues: 1.1475 ------------------------------------------------------------------------------- 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: 0.5980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 814 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5396 Z= 0.182 Angle : 0.418 4.665 7300 Z= 0.220 Chirality : 0.037 0.136 849 Planarity : 0.004 0.032 905 Dihedral : 13.670 177.915 754 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.86 % Allowed : 9.33 % Favored : 89.81 % 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: 1.19 (0.33), residues: 639 helix: 1.94 (0.27), residues: 381 sheet: 0.80 (0.81), residues: 46 loop : -1.41 (0.39), residues: 212 *********************** 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 40 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.594 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 40 average time/residue: 0.1773 time to fit residues: 9.8269 Evaluate side-chains 33 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0518 time to fit residues: 0.9139 ------------------------------------------------------------------------------- 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: 0.9990 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5396 Z= 0.220 Angle : 0.435 4.706 7300 Z= 0.228 Chirality : 0.038 0.185 849 Planarity : 0.004 0.033 905 Dihedral : 13.570 177.118 754 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.52 % Allowed : 10.36 % Favored : 89.12 % 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: 1.16 (0.33), residues: 639 helix: 1.93 (0.27), residues: 377 sheet: 0.77 (0.80), residues: 46 loop : -1.39 (0.39), residues: 216 *********************** 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: 3 poor density : 34 time to evaluate : 0.606 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 0.2045 time to fit residues: 10.3052 Evaluate side-chains 32 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 30 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0702 time to fit residues: 1.0701 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7017 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5396 Z= 0.183 Angle : 0.414 4.627 7300 Z= 0.218 Chirality : 0.037 0.162 849 Planarity : 0.003 0.033 905 Dihedral : 13.345 172.133 754 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.35 % Allowed : 10.71 % Favored : 88.95 % 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: 1.28 (0.33), residues: 639 helix: 2.02 (0.27), residues: 377 sheet: 0.81 (0.81), residues: 46 loop : -1.33 (0.39), residues: 216 *********************** 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 31 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 29 time to evaluate : 0.615 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.1855 time to fit residues: 8.1811 Evaluate side-chains 30 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 29 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0542 time to fit residues: 1.0643 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.0170 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5396 Z= 0.163 Angle : 0.405 4.646 7300 Z= 0.212 Chirality : 0.037 0.155 849 Planarity : 0.003 0.033 905 Dihedral : 13.112 171.498 754 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % 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: 1.33 (0.34), residues: 639 helix: 2.05 (0.27), residues: 378 sheet: 0.92 (0.81), residues: 46 loop : -1.34 (0.40), residues: 215 *********************** 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: 0 poor density : 33 time to evaluate : 0.599 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.1705 time to fit residues: 8.0321 Evaluate side-chains 31 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.581 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7587 ------------------------------------------------------------------------------- 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: 0.0050 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5396 Z= 0.136 Angle : 0.391 4.568 7300 Z= 0.205 Chirality : 0.036 0.148 849 Planarity : 0.003 0.034 905 Dihedral : 12.913 170.693 754 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % 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: 1.42 (0.34), residues: 639 helix: 2.11 (0.27), residues: 380 sheet: 1.06 (0.83), residues: 46 loop : -1.32 (0.40), residues: 213 *********************** 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 35 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.582 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.1626 time to fit residues: 8.2849 Evaluate side-chains 31 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.7988 ------------------------------------------------------------------------------- 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: 0.8980 chunk 59 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 31 optimal weight: 0.0030 chunk 40 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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: 0.7010 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5396 Z= 0.166 Angle : 0.409 7.587 7300 Z= 0.212 Chirality : 0.037 0.151 849 Planarity : 0.003 0.033 905 Dihedral : 12.866 171.473 754 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.17 % Allowed : 11.05 % Favored : 88.77 % 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: 1.44 (0.34), residues: 639 helix: 2.17 (0.27), residues: 379 sheet: 1.05 (0.83), residues: 46 loop : -1.37 (0.40), residues: 214 ********************** 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 32 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.618 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.1745 time to fit residues: 7.9943 Evaluate side-chains 32 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.564 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0550 time to fit residues: 0.8935 ------------------------------------------------------------------------------- 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: 0.9990 chunk 6 optimal weight: 0.0370 chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9464 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091305 restraints weight = 7962.514| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.12 r_work: 0.2955 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5396 Z= 0.227 Angle : 0.438 5.472 7300 Z= 0.229 Chirality : 0.038 0.159 849 Planarity : 0.004 0.033 905 Dihedral : 12.943 172.817 754 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.17 % Allowed : 11.23 % Favored : 88.60 % 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: 1.33 (0.34), residues: 639 helix: 2.02 (0.27), residues: 379 sheet: 1.06 (0.83), residues: 46 loop : -1.31 (0.41), residues: 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1496.96 seconds wall clock time: 27 minutes 44.77 seconds (1664.77 seconds total)