Starting phenix.real_space_refine on Tue Feb 13 10:33:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/02_2024/8e4y_27898_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/02_2024/8e4y_27898.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/02_2024/8e4y_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_27898/02_2024/8e4y_27898_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/02_2024/8e4y_27898_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/02_2024/8e4y_27898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/02_2024/8e4y_27898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/02_2024/8e4y_27898_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e4y_27898/02_2024/8e4y_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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3.35, per 1000 atoms: 0.63 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: 1.92 Conformation dependent library (CDL) restraints added in 925.9 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: 1.30 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: 1.46 Time building geometry restraints manager: 2.09 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: 2.560 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: 12.030 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 19.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.660 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 202 HIS 0.007 0.002 HIS A 496 PHE 0.022 0.002 PHE A 200 TYR 0.024 0.002 TYR A 292 ARG 0.004 0.001 ARG A 397 *********************** 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 : 0.710 Fit side-chains REVERT: A 169 LYS cc_start: 0.7978 (tttm) cc_final: 0.7752 (tptm) REVERT: A 172 ARG cc_start: 0.7571 (ttp-170) cc_final: 0.7359 (tmm160) REVERT: A 315 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7433 (mt-10) REVERT: A 347 ILE cc_start: 0.7876 (mt) cc_final: 0.7610 (tt) REVERT: A 357 ASP cc_start: 0.8033 (t0) cc_final: 0.7716 (t0) REVERT: A 426 GLN cc_start: 0.8146 (tp40) cc_final: 0.7629 (mt0) REVERT: A 470 GLU cc_start: 0.7623 (tt0) cc_final: 0.7222 (tt0) REVERT: A 520 ASP cc_start: 0.8492 (t70) cc_final: 0.8063 (m-30) REVERT: A 555 PHE cc_start: 0.7791 (m-80) cc_final: 0.7483 (m-10) REVERT: A 582 MET cc_start: 0.7754 (mmm) cc_final: 0.7441 (mmm) REVERT: A 705 TYR cc_start: 0.7678 (m-80) cc_final: 0.7467 (m-80) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2452 time to fit residues: 22.5839 Evaluate side-chains 42 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.650 ------------------------------------------------------------------------------- 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: 1.9990 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: 1.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 714 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.2121 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= 0.178 Angle : 0.486 5.227 7300 Z= 0.263 Chirality : 0.038 0.160 849 Planarity : 0.004 0.036 905 Dihedral : 14.561 176.931 754 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.07 % Allowed : 7.08 % Favored : 90.85 % 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: 0.17 (0.32), residues: 639 helix: 1.08 (0.26), residues: 377 sheet: -0.33 (0.66), residues: 57 loop : -1.54 (0.38), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 202 HIS 0.003 0.001 HIS A 297 PHE 0.019 0.001 PHE A 200 TYR 0.014 0.002 TYR A 292 ARG 0.002 0.000 ARG A 138 *********************** 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 59 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.646 Fit side-chains REVERT: A 105 LEU cc_start: 0.7669 (tt) cc_final: 0.7376 (mm) REVERT: A 172 ARG cc_start: 0.7545 (ttp-170) cc_final: 0.7343 (tmm160) REVERT: A 289 ASP cc_start: 0.6351 (t0) cc_final: 0.5864 (t0) REVERT: A 357 ASP cc_start: 0.7792 (t0) cc_final: 0.7583 (t0) REVERT: A 426 GLN cc_start: 0.8155 (tp40) cc_final: 0.7523 (mt0) REVERT: A 520 ASP cc_start: 0.8414 (t70) cc_final: 0.7875 (m-30) REVERT: A 555 PHE cc_start: 0.8072 (m-80) cc_final: 0.7812 (m-10) REVERT: A 566 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6698 (t) outliers start: 12 outliers final: 6 residues processed: 58 average time/residue: 0.1969 time to fit residues: 14.9099 Evaluate side-chains 48 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 HIS Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 823 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 49 optimal weight: 0.1980 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 365 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5396 Z= 0.172 Angle : 0.431 6.610 7300 Z= 0.229 Chirality : 0.037 0.138 849 Planarity : 0.004 0.034 905 Dihedral : 14.077 173.665 754 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.07 % Allowed : 8.64 % 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: 0.91 (0.33), residues: 639 helix: 1.73 (0.26), residues: 380 sheet: -0.06 (0.69), residues: 58 loop : -1.42 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.003 0.001 HIS A 578 PHE 0.014 0.001 PHE A 274 TYR 0.011 0.001 TYR A 292 ARG 0.002 0.000 ARG A 138 *********************** 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 53 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 41 time to evaluate : 0.655 Fit side-chains REVERT: A 105 LEU cc_start: 0.7727 (tt) cc_final: 0.7422 (mm) REVERT: A 202 TRP cc_start: 0.7456 (OUTLIER) cc_final: 0.7066 (t60) REVERT: A 357 ASP cc_start: 0.7878 (t0) cc_final: 0.7642 (t0) REVERT: A 426 GLN cc_start: 0.8218 (tp40) cc_final: 0.7623 (mt0) REVERT: A 520 ASP cc_start: 0.8413 (t70) cc_final: 0.7876 (m-30) REVERT: A 531 ASP cc_start: 0.7768 (t0) cc_final: 0.7481 (t0) REVERT: A 555 PHE cc_start: 0.8088 (m-80) cc_final: 0.7773 (m-10) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.1628 time to fit residues: 11.8130 Evaluate side-chains 47 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 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 A 365 ASN A 715 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5396 Z= 0.184 Angle : 0.433 7.380 7300 Z= 0.226 Chirality : 0.038 0.166 849 Planarity : 0.004 0.034 905 Dihedral : 13.868 173.714 754 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.59 % Allowed : 8.81 % 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: 1.12 (0.33), residues: 639 helix: 1.97 (0.27), residues: 375 sheet: 0.12 (0.69), residues: 58 loop : -1.43 (0.39), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.004 0.001 HIS A 363 PHE 0.013 0.001 PHE A 200 TYR 0.011 0.001 TYR A 572 ARG 0.004 0.000 ARG A 278 *********************** 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 53 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 38 time to evaluate : 0.588 Fit side-chains REVERT: A 105 LEU cc_start: 0.7758 (tt) cc_final: 0.7445 (mm) REVERT: A 202 TRP cc_start: 0.7453 (OUTLIER) cc_final: 0.7037 (t60) REVERT: A 426 GLN cc_start: 0.8210 (tp40) cc_final: 0.7623 (mt0) REVERT: A 520 ASP cc_start: 0.8460 (t70) cc_final: 0.7905 (m-30) REVERT: A 531 ASP cc_start: 0.7762 (t0) cc_final: 0.7464 (t0) REVERT: A 555 PHE cc_start: 0.8112 (m-80) cc_final: 0.7740 (m-10) outliers start: 15 outliers final: 12 residues processed: 52 average time/residue: 0.1385 time to fit residues: 10.4911 Evaluate side-chains 51 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 365 ASN A 756 HIS A 814 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5396 Z= 0.270 Angle : 0.467 7.283 7300 Z= 0.242 Chirality : 0.039 0.163 849 Planarity : 0.004 0.036 905 Dihedral : 13.855 175.104 754 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.76 % Allowed : 8.98 % Favored : 88.26 % 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: 1.00 (0.33), residues: 639 helix: 1.86 (0.27), residues: 375 sheet: 0.61 (0.81), residues: 46 loop : -1.52 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.005 0.001 HIS A 363 PHE 0.018 0.001 PHE A 200 TYR 0.013 0.002 TYR A 572 ARG 0.002 0.000 ARG A 138 *********************** 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 52 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 36 time to evaluate : 0.672 Fit side-chains REVERT: A 105 LEU cc_start: 0.7742 (tt) cc_final: 0.7401 (mm) REVERT: A 202 TRP cc_start: 0.7455 (OUTLIER) cc_final: 0.7040 (t60) REVERT: A 426 GLN cc_start: 0.8247 (tp40) cc_final: 0.7631 (mt0) REVERT: A 520 ASP cc_start: 0.8513 (t70) cc_final: 0.7948 (m-30) REVERT: A 531 ASP cc_start: 0.7771 (t0) cc_final: 0.7475 (t0) REVERT: A 555 PHE cc_start: 0.8157 (m-80) cc_final: 0.7788 (m-10) outliers start: 16 outliers final: 12 residues processed: 51 average time/residue: 0.1526 time to fit residues: 11.2208 Evaluate side-chains 49 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 36 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 767 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL 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: 0.6980 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 62 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** 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: 0.7014 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5396 Z= 0.147 Angle : 0.411 6.619 7300 Z= 0.216 Chirality : 0.037 0.148 849 Planarity : 0.003 0.034 905 Dihedral : 13.645 177.410 754 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.25 % Allowed : 9.50 % Favored : 88.26 % 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: 1.22 (0.33), residues: 639 helix: 2.06 (0.27), residues: 375 sheet: 0.78 (0.81), residues: 46 loop : -1.50 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 104 HIS 0.003 0.001 HIS A 578 PHE 0.012 0.001 PHE A 200 TYR 0.010 0.001 TYR A 292 ARG 0.002 0.000 ARG A 138 *********************** 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 51 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.684 Fit side-chains REVERT: A 105 LEU cc_start: 0.7739 (tt) cc_final: 0.7407 (mm) REVERT: A 202 TRP cc_start: 0.7514 (OUTLIER) cc_final: 0.7078 (t60) REVERT: A 426 GLN cc_start: 0.8260 (tp40) cc_final: 0.7672 (mt0) REVERT: A 520 ASP cc_start: 0.8532 (t70) cc_final: 0.7918 (m-30) REVERT: A 531 ASP cc_start: 0.7848 (t0) cc_final: 0.7555 (t0) REVERT: A 555 PHE cc_start: 0.8215 (m-80) cc_final: 0.7830 (m-10) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.1673 time to fit residues: 11.5899 Evaluate side-chains 44 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 35 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 814 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.3229 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= 0.204 Angle : 0.435 6.431 7300 Z= 0.225 Chirality : 0.038 0.156 849 Planarity : 0.004 0.033 905 Dihedral : 13.536 177.555 754 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.25 % Allowed : 9.84 % Favored : 87.91 % 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: 2.00 (0.27), residues: 375 sheet: 0.84 (0.83), residues: 46 loop : -1.52 (0.38), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 202 HIS 0.005 0.001 HIS A 363 PHE 0.015 0.001 PHE A 200 TYR 0.011 0.001 TYR A 572 ARG 0.006 0.000 ARG A 278 *********************** 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 47 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 34 time to evaluate : 0.605 Fit side-chains REVERT: A 105 LEU cc_start: 0.7757 (tt) cc_final: 0.7387 (mm) REVERT: A 202 TRP cc_start: 0.7589 (OUTLIER) cc_final: 0.7171 (t60) REVERT: A 520 ASP cc_start: 0.8570 (t70) cc_final: 0.7980 (m-30) REVERT: A 531 ASP cc_start: 0.7837 (t0) cc_final: 0.7554 (t0) REVERT: A 555 PHE cc_start: 0.8212 (m-80) cc_final: 0.7782 (m-10) outliers start: 13 outliers final: 9 residues processed: 46 average time/residue: 0.1743 time to fit residues: 11.1702 Evaluate side-chains 42 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL 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: 0.9980 chunk 42 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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: 0.7035 moved from start: 0.3305 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= 0.230 Angle : 0.442 6.404 7300 Z= 0.229 Chirality : 0.038 0.155 849 Planarity : 0.004 0.034 905 Dihedral : 13.450 174.077 754 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.90 % Allowed : 9.67 % Favored : 88.43 % 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: 1.15 (0.33), residues: 639 helix: 1.96 (0.27), residues: 375 sheet: 0.84 (0.83), residues: 46 loop : -1.47 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 202 HIS 0.003 0.001 HIS A 363 PHE 0.018 0.001 PHE A 200 TYR 0.011 0.001 TYR A 572 ARG 0.006 0.000 ARG A 278 *********************** 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 44 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.588 Fit side-chains REVERT: A 105 LEU cc_start: 0.7657 (tt) cc_final: 0.7276 (mm) REVERT: A 202 TRP cc_start: 0.7556 (OUTLIER) cc_final: 0.7127 (t60) REVERT: A 520 ASP cc_start: 0.8583 (t70) cc_final: 0.7993 (m-30) REVERT: A 531 ASP cc_start: 0.7831 (t0) cc_final: 0.7556 (t0) REVERT: A 555 PHE cc_start: 0.8199 (m-80) cc_final: 0.7736 (m-10) outliers start: 11 outliers final: 9 residues processed: 43 average time/residue: 0.1538 time to fit residues: 9.3947 Evaluate side-chains 42 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5396 Z= 0.267 Angle : 0.460 6.602 7300 Z= 0.237 Chirality : 0.038 0.156 849 Planarity : 0.004 0.035 905 Dihedral : 13.423 173.623 754 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.07 % Allowed : 9.67 % Favored : 88.26 % 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: 1.09 (0.34), residues: 639 helix: 1.92 (0.27), residues: 374 sheet: 0.82 (0.84), residues: 46 loop : -1.50 (0.39), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 202 HIS 0.004 0.001 HIS A 363 PHE 0.020 0.001 PHE A 200 TYR 0.012 0.001 TYR A 572 ARG 0.005 0.000 ARG A 278 *********************** 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 45 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 33 time to evaluate : 0.690 Fit side-chains REVERT: A 105 LEU cc_start: 0.7659 (tt) cc_final: 0.7245 (mm) REVERT: A 202 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.7088 (t60) REVERT: A 520 ASP cc_start: 0.8602 (t70) cc_final: 0.8000 (m-30) REVERT: A 531 ASP cc_start: 0.7824 (t0) cc_final: 0.7552 (t0) outliers start: 12 outliers final: 8 residues processed: 43 average time/residue: 0.1627 time to fit residues: 9.9962 Evaluate side-chains 41 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 32 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 299 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3465 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= 0.254 Angle : 0.460 6.585 7300 Z= 0.237 Chirality : 0.038 0.164 849 Planarity : 0.004 0.035 905 Dihedral : 13.233 172.853 754 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.90 % Allowed : 9.84 % Favored : 88.26 % 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 (0.34), residues: 639 helix: 1.87 (0.27), residues: 372 sheet: 0.90 (0.85), residues: 46 loop : -1.40 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.004 0.001 HIS A 363 PHE 0.019 0.001 PHE A 200 TYR 0.012 0.001 TYR A 572 ARG 0.005 0.000 ARG A 278 ********************** 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 43 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.665 Fit side-chains REVERT: A 105 LEU cc_start: 0.7674 (tt) cc_final: 0.7213 (mm) REVERT: A 202 TRP cc_start: 0.7527 (OUTLIER) cc_final: 0.7073 (t60) REVERT: A 520 ASP cc_start: 0.8569 (t70) cc_final: 0.7998 (m-30) outliers start: 11 outliers final: 8 residues processed: 41 average time/residue: 0.1573 time to fit residues: 9.3029 Evaluate side-chains 40 residues out of total 579 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASN Chi-restraints excluded: chain A residue 202 TRP Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 706 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 826 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 45 optimal weight: 0.2980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.110337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.091379 restraints weight = 7933.072| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.03 r_work: 0.2954 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5396 Z= 0.176 Angle : 0.956 55.102 7300 Z= 0.567 Chirality : 0.038 0.171 849 Planarity : 0.004 0.034 905 Dihedral : 13.223 173.045 754 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.73 % Allowed : 10.02 % Favored : 88.26 % 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: 1.15 (0.34), residues: 639 helix: 1.94 (0.27), residues: 372 sheet: 0.92 (0.85), residues: 46 loop : -1.39 (0.40), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.004 0.001 HIS A 363 PHE 0.020 0.001 PHE A 200 TYR 0.011 0.001 TYR A 572 ARG 0.005 0.000 ARG A 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1508.49 seconds wall clock time: 27 minutes 54.79 seconds (1674.79 seconds total)