Starting phenix.real_space_refine on Wed Jul 1 23:39:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8hnh_34913/07_2026/8hnh_34913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnh_34913/07_2026/8hnh_34913.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2026/8hnh_34913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2026/8hnh_34913.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2026/8hnh_34913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2026/8hnh_34913.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2026/8hnh_34913.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2026/8hnh_34913.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.041 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 2797 2.51 5 N 668 2.21 5 O 737 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4236 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4142 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 77} Link IDs: {'PTRANS': 20, 'TRANS': 542} Chain breaks: 3 Unresolved non-hydrogen bonds: 245 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'HIS:plan': 2, 'ARG:plan': 4, 'GLU:plan': 5, 'TYR:plan': 4, 'ASP:plan': 5, 'ASN:plan1': 10, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 133 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'30B': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.18, per 1000 atoms: 0.28 Number of scatterers: 4236 At special positions: 0 Unit cell: (56.576, 98.176, 84.032, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 737 8.00 N 668 7.00 C 2797 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.04 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 802 " - " ASN A 516 " " NAG B 1 " - " ASN A 503 " Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 166.0 milliseconds 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 71.2% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 26 through 60 removed outlier: 4.407A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 33 " --> pdb=" O MET A 29 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ILE A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N HIS A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 91 removed outlier: 3.645A pdb=" N GLY A 67 " --> pdb=" O SER A 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 68 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 86 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 89 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A 90 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 112 removed outlier: 3.730A pdb=" N LEU A 96 " --> pdb=" O HIS A 92 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 118 removed outlier: 4.249A pdb=" N PHE A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 166 removed outlier: 3.506A pdb=" N SER A 166 " --> pdb=" O CYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.929A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 175 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 182 " --> pdb=" O ASN A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 200 removed outlier: 3.554A pdb=" N ILE A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASP A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 199 " --> pdb=" O TYR A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 233 removed outlier: 4.049A pdb=" N ILE A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLY A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) Proline residue: A 220 - end of helix Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.817A pdb=" N SER A 265 " --> pdb=" O ASN A 261 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Proline residue: A 275 - end of helix removed outlier: 4.301A pdb=" N PHE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 333 removed outlier: 3.667A pdb=" N LEU A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 368 removed outlier: 3.564A pdb=" N MET A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 400 removed outlier: 4.205A pdb=" N ILE A 376 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LEU A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL A 380 " --> pdb=" O ILE A 376 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ILE A 383 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 403 through 425 removed outlier: 3.874A pdb=" N TYR A 425 " --> pdb=" O PHE A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 463 removed outlier: 4.202A pdb=" N CYS A 463 " --> pdb=" O CYS A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 527 through 563 removed outlier: 3.655A pdb=" N ARG A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 551 " --> pdb=" O PHE A 547 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N THR A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N SER A 554 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N HIS A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N VAL A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 566 No H-bonds generated for 'chain 'A' and resid 564 through 566' Processing helix chain 'A' and resid 567 through 583 Processing helix chain 'A' and resid 585 through 597 removed outlier: 3.644A pdb=" N ILE A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 597 " --> pdb=" O ALA A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 651 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 removed outlier: 3.537A pdb=" N TYR A 481 " --> pdb=" O VAL A 473 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 473 " --> pdb=" O TYR A 481 " (cutoff:3.500A) 258 hydrogen bonds defined for protein. 774 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: 0.62 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 626 1.31 - 1.44: 1242 1.44 - 1.56: 2422 1.56 - 1.69: 2 1.69 - 1.81: 51 Bond restraints: 4343 Sorted by residual: bond pdb=" C9 30B A 801 " pdb=" N13 30B A 801 " ideal model delta sigma weight residual 1.347 1.490 -0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" C4 NAG B 1 " pdb=" O4 NAG B 1 " ideal model delta sigma weight residual 1.409 1.547 -0.138 2.00e-02 2.50e+03 4.73e+01 bond pdb=" CA GLU A 202 " pdb=" C GLU A 202 " ideal model delta sigma weight residual 1.528 1.573 -0.045 8.80e-03 1.29e+04 2.65e+01 bond pdb=" CG ASN A 213 " pdb=" ND2 ASN A 213 " ideal model delta sigma weight residual 1.328 1.228 0.100 2.10e-02 2.27e+03 2.27e+01 bond pdb=" CG ASN A 213 " pdb=" OD1 ASN A 213 " ideal model delta sigma weight residual 1.231 1.321 -0.090 1.90e-02 2.77e+03 2.25e+01 ... (remaining 4338 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.11: 5638 3.11 - 6.21: 235 6.21 - 9.32: 24 9.32 - 12.42: 4 12.42 - 15.53: 5 Bond angle restraints: 5906 Sorted by residual: angle pdb=" N TYR A 338 " pdb=" CA TYR A 338 " pdb=" C TYR A 338 " ideal model delta sigma weight residual 111.36 119.22 -7.86 1.09e+00 8.42e-01 5.19e+01 angle pdb=" N THR A 382 " pdb=" CA THR A 382 " pdb=" C THR A 382 " ideal model delta sigma weight residual 111.28 118.46 -7.18 1.09e+00 8.42e-01 4.34e+01 angle pdb=" N ILE A 585 " pdb=" CA ILE A 585 " pdb=" C ILE A 585 " ideal model delta sigma weight residual 111.56 117.20 -5.64 8.60e-01 1.35e+00 4.30e+01 angle pdb=" C VAL A 189 " pdb=" N PRO A 190 " pdb=" CA PRO A 190 " ideal model delta sigma weight residual 118.97 112.63 6.34 1.04e+00 9.25e-01 3.72e+01 angle pdb=" N GLN A 366 " pdb=" CA GLN A 366 " pdb=" C GLN A 366 " ideal model delta sigma weight residual 111.36 117.92 -6.56 1.09e+00 8.42e-01 3.62e+01 ... (remaining 5901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.44: 2421 29.44 - 58.88: 84 58.88 - 88.32: 17 88.32 - 117.76: 0 117.76 - 147.20: 3 Dihedral angle restraints: 2525 sinusoidal: 918 harmonic: 1607 Sorted by residual: dihedral pdb=" CB CYS A 142 " pdb=" SG CYS A 142 " pdb=" SG CYS A 463 " pdb=" CB CYS A 463 " ideal model delta sinusoidal sigma weight residual -86.00 -127.20 41.20 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CB CYS A 430 " pdb=" SG CYS A 430 " pdb=" SG CYS A 530 " pdb=" CB CYS A 530 " ideal model delta sinusoidal sigma weight residual 93.00 132.66 -39.66 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" C14 30B A 801 " pdb=" C19 30B A 801 " pdb=" C20 30B A 801 " pdb=" C21 30B A 801 " ideal model delta sinusoidal sigma weight residual 80.82 -131.98 -147.20 1 3.00e+01 1.11e-03 1.96e+01 ... (remaining 2522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.305: 683 0.305 - 0.610: 6 0.610 - 0.915: 1 0.915 - 1.220: 0 1.220 - 1.525: 1 Chirality restraints: 691 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-02 2.50e+03 1.37e+03 chirality pdb=" C1 NAG A 802 " pdb=" ND2 ASN A 516 " pdb=" C2 NAG A 802 " pdb=" O5 NAG A 802 " both_signs ideal model delta sigma weight residual False -2.40 -0.88 -1.52 2.00e-01 2.50e+01 5.81e+01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 503 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.94 0.54 2.00e-01 2.50e+01 7.29e+00 ... (remaining 688 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.313 2.00e-02 2.50e+03 2.66e-01 8.82e+02 pdb=" C7 NAG B 2 " -0.078 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.463 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 503 " -0.232 2.00e-02 2.50e+03 2.47e-01 7.64e+02 pdb=" CG ASN A 503 " 0.085 2.00e-02 2.50e+03 pdb=" OD1 ASN A 503 " 0.096 2.00e-02 2.50e+03 pdb=" ND2 ASN A 503 " 0.368 2.00e-02 2.50e+03 pdb=" C1 NAG B 1 " -0.317 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.164 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C7 NAG B 1 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " 0.037 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.224 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.129 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 559 2.75 - 3.28: 4719 3.28 - 3.82: 6581 3.82 - 4.36: 7622 4.36 - 4.90: 12950 Nonbonded interactions: 32431 Sorted by model distance: nonbonded pdb=" CE1 PHE A 116 " pdb=" CZ3 TRP A 259 " model vdw 2.207 3.640 nonbonded pdb=" CE1 PHE A 116 " pdb=" CE3 TRP A 259 " model vdw 2.218 3.640 nonbonded pdb=" NH1 ARG A 57 " pdb=" O SER A 252 " model vdw 2.219 3.120 nonbonded pdb=" OE1 GLN A 366 " pdb=" OG SER A 618 " model vdw 2.291 3.040 nonbonded pdb=" CZ PHE A 116 " pdb=" CE3 TRP A 259 " model vdw 2.422 3.640 ... (remaining 32426 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.910 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 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 : 0.009 0.143 4353 Z= 0.580 Angle : 1.572 29.345 5929 Z= 0.966 Chirality : 0.106 1.525 691 Planarity : 0.015 0.266 718 Dihedral : 16.417 147.199 1482 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.67 % Allowed : 14.91 % Favored : 81.42 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.33), residues: 555 helix: 2.38 (0.27), residues: 327 sheet: None (None), residues: 0 loop : -0.69 (0.33), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.025 0.002 TYR A 590 PHE 0.020 0.002 PHE A 341 TRP 0.019 0.002 TRP A 259 HIS 0.005 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00872 / 0.57 ( 4343) covalent geometry : angle 1.44444 / 0.95 ( 5906) SS BOND : bond 0.00398 / 0.21 ( 7) SS BOND : angle 0.84214 / 0.58 ( 14) hydrogen bonds : bond 0.24573 / 16.38 ( 258) hydrogen bonds : angle 7.90949 / 6.06 ( 774) link_BETA1-4 : bond 0.08095 / 4.26 ( 1) link_BETA1-4 : angle 18.44695 / 11.10 ( 3) link_NAG-ASN : bond 0.08868 / 4.66 ( 2) link_NAG-ASN : angle 14.70656 / 13.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 345 THR cc_start: 0.8029 (t) cc_final: 0.6892 (p) REVERT: A 648 LYS cc_start: 0.8875 (ttpt) cc_final: 0.8482 (ttpp) outliers start: 15 outliers final: 7 residues processed: 100 average time/residue: 0.0718 time to fit residues: 9.1133 Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 639 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.0570 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.236933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.195192 restraints weight = 4016.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.197532 restraints weight = 2939.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.199648 restraints weight = 2386.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.200681 restraints weight = 2092.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.201024 restraints weight = 1907.149| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4353 Z= 0.167 Angle : 0.788 15.107 5929 Z= 0.361 Chirality : 0.048 0.272 691 Planarity : 0.005 0.057 718 Dihedral : 16.282 170.788 670 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.93 % Allowed : 19.07 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.34), residues: 555 helix: 2.24 (0.26), residues: 351 sheet: None (None), residues: 0 loop : -0.46 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 57 TYR 0.016 0.002 TYR A 590 PHE 0.016 0.002 PHE A 73 TRP 0.015 0.001 TRP A 171 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 ( 4343) covalent geometry : angle 0.74836 / 0.35 ( 5906) SS BOND : bond 0.00252 / 0.12 ( 7) SS BOND : angle 0.66954 / 0.42 ( 14) hydrogen bonds : bond 0.06008 / 4.00 ( 258) hydrogen bonds : angle 5.10561 / 3.90 ( 774) link_BETA1-4 : bond 0.01843 / 0.97 ( 1) link_BETA1-4 : angle 9.35750 / 5.37 ( 3) link_NAG-ASN : bond 0.01665 / 0.87 ( 2) link_NAG-ASN : angle 4.24843 / 3.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 LYS cc_start: 0.8745 (ttpt) cc_final: 0.8412 (ttpp) outliers start: 12 outliers final: 7 residues processed: 74 average time/residue: 0.0760 time to fit residues: 7.1283 Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 46 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.259122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.206081 restraints weight = 4842.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.211150 restraints weight = 2878.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.214559 restraints weight = 2049.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.216659 restraints weight = 1661.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.217633 restraints weight = 1455.227| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4353 Z= 0.152 Angle : 0.703 12.574 5929 Z= 0.321 Chirality : 0.047 0.376 691 Planarity : 0.004 0.051 718 Dihedral : 15.546 169.383 665 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.42 % Allowed : 18.58 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.34), residues: 555 helix: 1.97 (0.26), residues: 360 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.020 0.002 TYR A 590 PHE 0.014 0.001 PHE A 73 TRP 0.012 0.001 TRP A 171 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 4343) covalent geometry : angle 0.67353 / 0.31 ( 5906) SS BOND : bond 0.00296 / 0.17 ( 7) SS BOND : angle 0.72222 / 0.41 ( 14) hydrogen bonds : bond 0.05087 / 3.41 ( 258) hydrogen bonds : angle 4.64803 / 3.52 ( 774) link_BETA1-4 : bond 0.01126 / 0.59 ( 1) link_BETA1-4 : angle 7.55238 / 4.15 ( 3) link_NAG-ASN : bond 0.01027 / 0.54 ( 2) link_NAG-ASN : angle 3.42384 / 3.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8041 (mm) cc_final: 0.7735 (mm) REVERT: A 198 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5904 (t0) REVERT: A 648 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8279 (ttpp) outliers start: 14 outliers final: 9 residues processed: 72 average time/residue: 0.0748 time to fit residues: 6.8478 Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 4.9990 chunk 14 optimal weight: 0.4980 chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.0470 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.260445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.207404 restraints weight = 4835.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.212485 restraints weight = 2873.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.215767 restraints weight = 2056.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.217648 restraints weight = 1668.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.219389 restraints weight = 1468.959| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4353 Z= 0.130 Angle : 0.648 11.680 5929 Z= 0.293 Chirality : 0.043 0.270 691 Planarity : 0.004 0.052 718 Dihedral : 14.864 168.002 661 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 2.69 % Allowed : 19.32 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.34), residues: 555 helix: 1.98 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.020 0.001 TYR A 590 PHE 0.011 0.001 PHE A 73 TRP 0.009 0.001 TRP A 171 HIS 0.002 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 4343) covalent geometry : angle 0.63000 / 0.29 ( 5906) SS BOND : bond 0.00207 / 0.11 ( 7) SS BOND : angle 0.60320 / 0.37 ( 14) hydrogen bonds : bond 0.04530 / 3.05 ( 258) hydrogen bonds : angle 4.36539 / 3.27 ( 774) link_BETA1-4 : bond 0.00693 / 0.36 ( 1) link_BETA1-4 : angle 5.67749 / 3.50 ( 3) link_NAG-ASN : bond 0.01557 / 0.82 ( 2) link_NAG-ASN : angle 2.69814 / 2.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 118 MET cc_start: 0.6523 (mpp) cc_final: 0.6267 (mpp) REVERT: A 181 ARG cc_start: 0.7705 (mtp85) cc_final: 0.7484 (ttp80) REVERT: A 198 ASP cc_start: 0.6187 (OUTLIER) cc_final: 0.5909 (t0) REVERT: A 591 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.5244 (t80) REVERT: A 648 LYS cc_start: 0.8565 (ttpt) cc_final: 0.8206 (ttpp) outliers start: 11 outliers final: 7 residues processed: 76 average time/residue: 0.0728 time to fit residues: 7.1100 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.258322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.205846 restraints weight = 4781.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.210794 restraints weight = 2858.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.213784 restraints weight = 2044.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.216258 restraints weight = 1660.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.217427 restraints weight = 1451.537| |-----------------------------------------------------------------------------| r_work (final): 0.4474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4353 Z= 0.142 Angle : 0.680 12.288 5929 Z= 0.310 Chirality : 0.044 0.251 691 Planarity : 0.004 0.051 718 Dihedral : 14.556 156.125 661 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.91 % Allowed : 20.05 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.34), residues: 555 helix: 1.90 (0.26), residues: 358 sheet: None (None), residues: 0 loop : -0.55 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 246 TYR 0.023 0.001 TYR A 590 PHE 0.010 0.001 PHE A 73 TRP 0.007 0.001 TRP A 254 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 ( 4343) covalent geometry : angle 0.65853 / 0.30 ( 5906) SS BOND : bond 0.00095 / 0.05 ( 7) SS BOND : angle 2.33540 / 1.35 ( 14) hydrogen bonds : bond 0.04472 / 3.01 ( 258) hydrogen bonds : angle 4.35435 / 3.26 ( 774) link_BETA1-4 : bond 0.00754 / 0.40 ( 1) link_BETA1-4 : angle 5.31009 / 3.02 ( 3) link_NAG-ASN : bond 0.00805 / 0.42 ( 2) link_NAG-ASN : angle 1.85489 / 1.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6666 (mpp) cc_final: 0.6365 (mpp) REVERT: A 181 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7477 (ttp80) REVERT: A 198 ASP cc_start: 0.6209 (OUTLIER) cc_final: 0.5861 (t0) REVERT: A 267 LEU cc_start: 0.6206 (OUTLIER) cc_final: 0.5464 (tt) REVERT: A 591 PHE cc_start: 0.7228 (OUTLIER) cc_final: 0.5198 (t80) REVERT: A 648 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8181 (ttpp) outliers start: 16 outliers final: 11 residues processed: 72 average time/residue: 0.0771 time to fit residues: 6.9719 Evaluate side-chains 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 215 ILE Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 41 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.0030 chunk 29 optimal weight: 0.0670 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.261244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.209154 restraints weight = 4819.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.214108 restraints weight = 2874.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.217378 restraints weight = 2054.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.219566 restraints weight = 1658.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.220610 restraints weight = 1452.441| |-----------------------------------------------------------------------------| r_work (final): 0.4498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4353 Z= 0.119 Angle : 0.634 11.999 5929 Z= 0.288 Chirality : 0.042 0.227 691 Planarity : 0.004 0.050 718 Dihedral : 14.146 155.143 661 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.42 % Allowed : 21.27 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.34), residues: 555 helix: 1.99 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.55 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 181 TYR 0.028 0.001 TYR A 590 PHE 0.010 0.001 PHE A 73 TRP 0.008 0.001 TRP A 171 HIS 0.001 0.000 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 ( 4343) covalent geometry : angle 0.62250 / 0.28 ( 5906) SS BOND : bond 0.00084 / 0.04 ( 7) SS BOND : angle 1.21106 / 0.68 ( 14) hydrogen bonds : bond 0.04110 / 2.76 ( 258) hydrogen bonds : angle 4.19029 / 3.13 ( 774) link_BETA1-4 : bond 0.00729 / 0.38 ( 1) link_BETA1-4 : angle 4.65830 / 2.65 ( 3) link_NAG-ASN : bond 0.00645 / 0.34 ( 2) link_NAG-ASN : angle 1.23986 / 1.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7454 (ttp80) REVERT: A 198 ASP cc_start: 0.5958 (OUTLIER) cc_final: 0.5691 (t0) REVERT: A 267 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.5468 (tt) REVERT: A 467 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: A 532 ARG cc_start: 0.6377 (tpp-160) cc_final: 0.6082 (mmt180) REVERT: A 557 MET cc_start: 0.8692 (tmm) cc_final: 0.8330 (tmm) REVERT: A 591 PHE cc_start: 0.7286 (OUTLIER) cc_final: 0.5553 (t80) REVERT: A 648 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8126 (ttpp) outliers start: 14 outliers final: 7 residues processed: 71 average time/residue: 0.0918 time to fit residues: 7.9685 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 1.9990 chunk 15 optimal weight: 0.0980 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 0.0040 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 20 optimal weight: 2.9990 overall best weight: 0.3650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.259551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.211607 restraints weight = 4184.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.214534 restraints weight = 3012.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.216796 restraints weight = 2404.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.217735 restraints weight = 2101.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.218610 restraints weight = 1947.227| |-----------------------------------------------------------------------------| r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4353 Z= 0.119 Angle : 0.636 12.032 5929 Z= 0.290 Chirality : 0.042 0.229 691 Planarity : 0.004 0.047 718 Dihedral : 13.637 147.261 661 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.18 % Allowed : 23.23 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.34), residues: 555 helix: 2.02 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.52 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.023 0.001 TYR A 590 PHE 0.008 0.001 PHE A 73 TRP 0.007 0.001 TRP A 171 HIS 0.001 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 4343) covalent geometry : angle 0.62559 / 0.29 ( 5906) SS BOND : bond 0.00095 / 0.05 ( 7) SS BOND : angle 1.21240 / 0.67 ( 14) hydrogen bonds : bond 0.04094 / 2.77 ( 258) hydrogen bonds : angle 4.15923 / 3.10 ( 774) link_BETA1-4 : bond 0.00721 / 0.38 ( 1) link_BETA1-4 : angle 4.32034 / 2.43 ( 3) link_NAG-ASN : bond 0.00590 / 0.31 ( 2) link_NAG-ASN : angle 1.17239 / 1.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6550 (OUTLIER) cc_final: 0.5825 (mpp) REVERT: A 181 ARG cc_start: 0.7686 (mtp85) cc_final: 0.7464 (ttp80) REVERT: A 267 LEU cc_start: 0.6397 (OUTLIER) cc_final: 0.5617 (tt) REVERT: A 467 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: A 532 ARG cc_start: 0.6346 (tpp-160) cc_final: 0.6080 (mmt180) REVERT: A 591 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.6023 (t80) REVERT: A 594 LEU cc_start: 0.6837 (tt) cc_final: 0.6446 (tp) REVERT: A 648 LYS cc_start: 0.8412 (ttpt) cc_final: 0.8113 (ttpp) outliers start: 13 outliers final: 7 residues processed: 69 average time/residue: 0.0785 time to fit residues: 6.6724 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4768 r_free = 0.4768 target = 0.259824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.207732 restraints weight = 4841.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.212621 restraints weight = 2892.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.215914 restraints weight = 2073.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.217796 restraints weight = 1681.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.218753 restraints weight = 1476.740| |-----------------------------------------------------------------------------| r_work (final): 0.4482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4353 Z= 0.136 Angle : 0.660 11.685 5929 Z= 0.297 Chirality : 0.044 0.338 691 Planarity : 0.004 0.047 718 Dihedral : 12.734 122.168 661 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.42 % Allowed : 23.72 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.66 (0.34), residues: 555 helix: 1.96 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.53 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.019 0.001 TYR A 590 PHE 0.010 0.001 PHE A 73 TRP 0.004 0.001 TRP A 259 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 4343) covalent geometry : angle 0.64326 / 0.29 ( 5906) SS BOND : bond 0.00098 / 0.05 ( 7) SS BOND : angle 1.19094 / 0.66 ( 14) hydrogen bonds : bond 0.04176 / 2.82 ( 258) hydrogen bonds : angle 4.16645 / 3.09 ( 774) link_BETA1-4 : bond 0.01218 / 0.64 ( 1) link_BETA1-4 : angle 3.94087 / 2.17 ( 3) link_NAG-ASN : bond 0.01117 / 0.59 ( 2) link_NAG-ASN : angle 3.38005 / 2.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6662 (OUTLIER) cc_final: 0.5862 (mpp) REVERT: A 267 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5518 (tt) REVERT: A 467 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: A 532 ARG cc_start: 0.6382 (tpp-160) cc_final: 0.6136 (mmt180) REVERT: A 591 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.5686 (t80) REVERT: A 594 LEU cc_start: 0.6884 (tt) cc_final: 0.6486 (tp) REVERT: A 648 LYS cc_start: 0.8394 (ttpt) cc_final: 0.7920 (tttm) outliers start: 14 outliers final: 9 residues processed: 70 average time/residue: 0.0780 time to fit residues: 6.7687 Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 0.5980 chunk 36 optimal weight: 9.9990 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 8.9990 chunk 48 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.258605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.206488 restraints weight = 4881.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.211299 restraints weight = 2946.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.214568 restraints weight = 2116.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.216371 restraints weight = 1716.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.217618 restraints weight = 1512.423| |-----------------------------------------------------------------------------| r_work (final): 0.4458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4353 Z= 0.143 Angle : 0.655 11.150 5929 Z= 0.301 Chirality : 0.044 0.372 691 Planarity : 0.004 0.048 718 Dihedral : 12.206 111.936 661 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.42 % Allowed : 23.47 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.34), residues: 555 helix: 1.87 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.50 (0.40), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 181 TYR 0.021 0.001 TYR A 616 PHE 0.009 0.001 PHE A 73 TRP 0.006 0.001 TRP A 259 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 4343) covalent geometry : angle 0.63916 / 0.30 ( 5906) SS BOND : bond 0.00099 / 0.05 ( 7) SS BOND : angle 1.12597 / 0.62 ( 14) hydrogen bonds : bond 0.04245 / 2.87 ( 258) hydrogen bonds : angle 4.19609 / 3.11 ( 774) link_BETA1-4 : bond 0.00938 / 0.49 ( 1) link_BETA1-4 : angle 3.74674 / 2.04 ( 3) link_NAG-ASN : bond 0.01178 / 0.62 ( 2) link_NAG-ASN : angle 3.36103 / 2.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6758 (OUTLIER) cc_final: 0.6384 (mpp) REVERT: A 181 ARG cc_start: 0.7659 (mtp85) cc_final: 0.7412 (ttp80) REVERT: A 467 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: A 532 ARG cc_start: 0.6385 (tpp-160) cc_final: 0.6131 (mmt180) REVERT: A 580 ARG cc_start: 0.7673 (mtp-110) cc_final: 0.7152 (mtm-85) REVERT: A 591 PHE cc_start: 0.7217 (OUTLIER) cc_final: 0.5162 (t80) REVERT: A 594 LEU cc_start: 0.6885 (tt) cc_final: 0.6568 (tp) REVERT: A 648 LYS cc_start: 0.8358 (ttpt) cc_final: 0.8063 (ttpp) outliers start: 14 outliers final: 11 residues processed: 67 average time/residue: 0.0837 time to fit residues: 7.0003 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.262816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.206969 restraints weight = 4895.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.212092 restraints weight = 2932.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.215149 restraints weight = 2121.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.217698 restraints weight = 1740.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.218835 restraints weight = 1529.881| |-----------------------------------------------------------------------------| r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4353 Z= 0.148 Angle : 0.652 11.451 5929 Z= 0.301 Chirality : 0.044 0.349 691 Planarity : 0.004 0.048 718 Dihedral : 12.278 111.004 661 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.42 % Allowed : 23.47 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.34), residues: 555 helix: 1.81 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.42 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.018 0.001 TYR A 169 PHE 0.011 0.001 PHE A 73 TRP 0.006 0.001 TRP A 259 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 4343) covalent geometry : angle 0.64094 / 0.30 ( 5906) SS BOND : bond 0.00203 / 0.10 ( 7) SS BOND : angle 1.11584 / 0.61 ( 14) hydrogen bonds : bond 0.04283 / 2.88 ( 258) hydrogen bonds : angle 4.23996 / 3.13 ( 774) link_BETA1-4 : bond 0.00903 / 0.48 ( 1) link_BETA1-4 : angle 3.35221 / 1.83 ( 3) link_NAG-ASN : bond 0.00865 / 0.45 ( 2) link_NAG-ASN : angle 2.61025 / 2.09 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6435 (mpp) REVERT: A 467 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: A 532 ARG cc_start: 0.6432 (tpp-160) cc_final: 0.6159 (mmt180) REVERT: A 580 ARG cc_start: 0.7675 (mtp-110) cc_final: 0.7173 (ttp-170) REVERT: A 594 LEU cc_start: 0.6990 (tt) cc_final: 0.6611 (tp) REVERT: A 648 LYS cc_start: 0.8359 (ttpt) cc_final: 0.8062 (ttpp) outliers start: 14 outliers final: 12 residues processed: 68 average time/residue: 0.0825 time to fit residues: 6.9538 Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 467 GLU Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 640 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 0.0170 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4819 r_free = 0.4819 target = 0.266006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.210448 restraints weight = 4871.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.215352 restraints weight = 2905.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.219231 restraints weight = 2096.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.221209 restraints weight = 1698.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.222491 restraints weight = 1496.112| |-----------------------------------------------------------------------------| r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4353 Z= 0.126 Angle : 0.652 11.290 5929 Z= 0.294 Chirality : 0.045 0.452 691 Planarity : 0.004 0.047 718 Dihedral : 12.263 112.008 661 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.93 % Allowed : 23.72 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.34), residues: 555 helix: 1.87 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.40 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 181 TYR 0.015 0.001 TYR A 616 PHE 0.014 0.001 PHE A 117 TRP 0.006 0.001 TRP A 171 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 4343) covalent geometry : angle 0.63363 / 0.29 ( 5906) SS BOND : bond 0.00082 / 0.04 ( 7) SS BOND : angle 0.95795 / 0.52 ( 14) hydrogen bonds : bond 0.04096 / 2.76 ( 258) hydrogen bonds : angle 4.13734 / 3.06 ( 774) link_BETA1-4 : bond 0.00485 / 0.26 ( 1) link_BETA1-4 : angle 3.58160 / 1.99 ( 3) link_NAG-ASN : bond 0.00839 / 0.44 ( 2) link_NAG-ASN : angle 4.05260 / 2.94 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 930.63 seconds wall clock time: 16 minutes 43.32 seconds (1003.32 seconds total)