Starting phenix.real_space_refine on Tue Mar 3 12:28:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnh_34913/03_2026/8hnh_34913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnh_34913/03_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_34913/03_2026/8hnh_34913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnh_34913/03_2026/8hnh_34913.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8hnh_34913/03_2026/8hnh_34913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnh_34913/03_2026/8hnh_34913.map" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.12, per 1000 atoms: 0.26 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: 0.38 Conformation dependent library (CDL) restraints added in 309.7 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: 0.13 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: 0.67 Time building geometry restraints manager: 0.51 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: 2470 29.44 - 58.88: 86 58.88 - 88.32: 25 88.32 - 117.76: 4 117.76 - 147.20: 3 Dihedral angle restraints: 2588 sinusoidal: 981 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 2585 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: 1.430 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.840 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 17.958 147.199 1545 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 covalent geometry : bond 0.00872 ( 4343) covalent geometry : angle 1.44444 ( 5906) SS BOND : bond 0.00398 ( 7) SS BOND : angle 0.84214 ( 14) hydrogen bonds : bond 0.24573 ( 258) hydrogen bonds : angle 7.90949 ( 774) link_BETA1-4 : bond 0.08095 ( 1) link_BETA1-4 : angle 18.44695 ( 3) link_NAG-ASN : bond 0.08868 ( 2) link_NAG-ASN : angle 14.70656 ( 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 : 0.122 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: 0.0656 time to fit residues: 8.3616 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 : 0.101 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4579 r_free = 0.4579 target = 0.236908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.194856 restraints weight = 4015.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.197428 restraints weight = 2949.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.199516 restraints weight = 2374.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.200485 restraints weight = 2076.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.200937 restraints weight = 1916.473| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4353 Z= 0.165 Angle : 0.804 14.595 5929 Z= 0.364 Chirality : 0.047 0.349 691 Planarity : 0.005 0.057 718 Dihedral : 17.088 170.581 733 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.38 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 : -0.45 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 181 TYR 0.017 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 covalent geometry : bond 0.00351 ( 4343) covalent geometry : angle 0.74438 ( 5906) SS BOND : bond 0.00276 ( 7) SS BOND : angle 0.60751 ( 14) hydrogen bonds : bond 0.06086 ( 258) hydrogen bonds : angle 5.11763 ( 774) link_BETA1-4 : bond 0.00751 ( 1) link_BETA1-4 : angle 9.17718 ( 3) link_NAG-ASN : bond 0.00794 ( 2) link_NAG-ASN : angle 7.08061 ( 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 : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8409 (ttpp) outliers start: 12 outliers final: 7 residues processed: 74 average time/residue: 0.0735 time to fit residues: 6.8144 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 : 0.151 ------------------------------------------------------------------------------- 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: 0.8980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4764 r_free = 0.4764 target = 0.258021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.205382 restraints weight = 4836.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.210475 restraints weight = 2878.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.213555 restraints weight = 2057.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.215979 restraints weight = 1674.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.216985 restraints weight = 1456.933| |-----------------------------------------------------------------------------| r_work (final): 0.4456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 4353 Z= 0.156 Angle : 0.760 18.314 5929 Z= 0.338 Chirality : 0.043 0.286 691 Planarity : 0.005 0.052 718 Dihedral : 15.485 169.417 728 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % 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: 1.64 (0.34), residues: 555 helix: 1.92 (0.26), residues: 360 sheet: None (None), residues: 0 loop : -0.47 (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 covalent geometry : bond 0.00357 ( 4343) covalent geometry : angle 0.67170 ( 5906) SS BOND : bond 0.00247 ( 7) SS BOND : angle 0.75146 ( 14) hydrogen bonds : bond 0.05190 ( 258) hydrogen bonds : angle 4.68440 ( 774) link_BETA1-4 : bond 0.01152 ( 1) link_BETA1-4 : angle 7.94201 ( 3) link_NAG-ASN : bond 0.01203 ( 2) link_NAG-ASN : angle 9.65409 ( 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 72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8025 (mm) cc_final: 0.7724 (mm) REVERT: A 198 ASP cc_start: 0.6204 (OUTLIER) cc_final: 0.5871 (t0) REVERT: A 648 LYS cc_start: 0.8681 (ttpt) cc_final: 0.8318 (ttpp) outliers start: 12 outliers final: 6 residues processed: 68 average time/residue: 0.0712 time to fit residues: 6.1996 Evaluate side-chains 66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.5980 chunk 33 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 28 optimal weight: 0.0030 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.259322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.206783 restraints weight = 4816.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.211862 restraints weight = 2877.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.215274 restraints weight = 2056.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.217255 restraints weight = 1658.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.218557 restraints weight = 1456.216| |-----------------------------------------------------------------------------| r_work (final): 0.4460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.3260 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= 0.134 Angle : 0.690 13.616 5929 Z= 0.306 Chirality : 0.041 0.245 691 Planarity : 0.005 0.052 718 Dihedral : 15.278 178.353 724 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.20 % Allowed : 19.80 % 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: 2.00 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.50 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 57 TYR 0.021 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 555 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4343) covalent geometry : angle 0.62917 ( 5906) SS BOND : bond 0.00257 ( 7) SS BOND : angle 0.60108 ( 14) hydrogen bonds : bond 0.04589 ( 258) hydrogen bonds : angle 4.38179 ( 774) link_BETA1-4 : bond 0.01039 ( 1) link_BETA1-4 : angle 6.93268 ( 3) link_NAG-ASN : bond 0.01142 ( 2) link_NAG-ASN : angle 7.52228 ( 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 75 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.154 Fit side-chains revert: symmetry clash REVERT: A 198 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.5948 (t0) REVERT: A 591 PHE cc_start: 0.7172 (OUTLIER) cc_final: 0.5086 (t80) REVERT: A 648 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8265 (ttpp) outliers start: 9 outliers final: 6 residues processed: 74 average time/residue: 0.0747 time to fit residues: 6.9273 Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.092 ------------------------------------------------------------------------------- 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 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: 0.3980 chunk 41 optimal weight: 0.0470 chunk 23 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.260148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.208320 restraints weight = 4789.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.213421 restraints weight = 2860.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.216444 restraints weight = 2038.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.218996 restraints weight = 1649.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.220287 restraints weight = 1431.243| |-----------------------------------------------------------------------------| r_work (final): 0.4495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.3617 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= 0.131 Angle : 0.722 15.099 5929 Z= 0.318 Chirality : 0.041 0.235 691 Planarity : 0.004 0.048 718 Dihedral : 14.964 171.819 724 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.67 % Allowed : 20.54 % Favored : 75.79 % 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: 1.65 (0.34), residues: 555 helix: 1.98 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.57 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 246 TYR 0.022 0.001 TYR A 590 PHE 0.010 0.001 PHE A 73 TRP 0.007 0.001 TRP A 171 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4343) covalent geometry : angle 0.64768 ( 5906) SS BOND : bond 0.00165 ( 7) SS BOND : angle 2.40395 ( 14) hydrogen bonds : bond 0.04369 ( 258) hydrogen bonds : angle 4.30312 ( 774) link_BETA1-4 : bond 0.00753 ( 1) link_BETA1-4 : angle 6.54406 ( 3) link_NAG-ASN : bond 0.01023 ( 2) link_NAG-ASN : angle 8.24306 ( 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 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7374 (ttp80) REVERT: A 198 ASP cc_start: 0.6108 (OUTLIER) cc_final: 0.5810 (t0) REVERT: A 267 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5457 (tt) REVERT: A 591 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.5328 (t80) REVERT: A 648 LYS cc_start: 0.8516 (ttpt) cc_final: 0.8158 (ttpp) outliers start: 15 outliers final: 8 residues processed: 77 average time/residue: 0.0644 time to fit residues: 6.2851 Evaluate side-chains 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.135 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 44 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 29 optimal weight: 0.0370 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4755 r_free = 0.4755 target = 0.256763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.206871 restraints weight = 4142.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.210747 restraints weight = 2727.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.213419 restraints weight = 2089.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.214849 restraints weight = 1758.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.216057 restraints weight = 1581.645| |-----------------------------------------------------------------------------| r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.3799 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= 0.131 Angle : 0.708 15.927 5929 Z= 0.310 Chirality : 0.041 0.248 691 Planarity : 0.004 0.049 718 Dihedral : 14.528 158.682 724 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.16 % Allowed : 20.78 % Favored : 75.06 % 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: 1.64 (0.34), residues: 555 helix: 1.98 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.59 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.031 0.001 TYR A 590 PHE 0.010 0.001 PHE A 73 TRP 0.006 0.001 TRP A 171 HIS 0.002 0.001 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4343) covalent geometry : angle 0.63667 ( 5906) SS BOND : bond 0.00089 ( 7) SS BOND : angle 1.54197 ( 14) hydrogen bonds : bond 0.04269 ( 258) hydrogen bonds : angle 4.25264 ( 774) link_BETA1-4 : bond 0.00688 ( 1) link_BETA1-4 : angle 6.23081 ( 3) link_NAG-ASN : bond 0.00594 ( 2) link_NAG-ASN : angle 8.42525 ( 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 78 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 61 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.5883 (OUTLIER) cc_final: 0.5621 (t0) REVERT: A 267 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5704 (tt) REVERT: A 467 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: A 532 ARG cc_start: 0.6478 (tpp-160) cc_final: 0.6153 (mmt180) REVERT: A 648 LYS cc_start: 0.8482 (ttpt) cc_final: 0.8169 (ttpp) outliers start: 17 outliers final: 11 residues processed: 75 average time/residue: 0.0926 time to fit residues: 8.4632 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 : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 53 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 20 optimal weight: 1.9990 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 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 = 0.4743 r_free = 0.4743 target = 0.255109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.207523 restraints weight = 4173.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.210534 restraints weight = 2976.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.212663 restraints weight = 2385.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.213012 restraints weight = 2067.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.213938 restraints weight = 1981.828| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3938 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= 0.141 Angle : 0.717 15.282 5929 Z= 0.313 Chirality : 0.041 0.211 691 Planarity : 0.004 0.049 718 Dihedral : 14.023 147.295 724 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.67 % Allowed : 22.00 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.91 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.58 (0.39), residues: 195 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 0.006 0.001 TRP A 254 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4343) covalent geometry : angle 0.65193 ( 5906) SS BOND : bond 0.00216 ( 7) SS BOND : angle 1.30492 ( 14) hydrogen bonds : bond 0.04310 ( 258) hydrogen bonds : angle 4.23738 ( 774) link_BETA1-4 : bond 0.00768 ( 1) link_BETA1-4 : angle 5.75363 ( 3) link_NAG-ASN : bond 0.01638 ( 2) link_NAG-ASN : angle 8.31755 ( 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: 15 poor density : 58 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.6021 (OUTLIER) cc_final: 0.5693 (t0) REVERT: A 467 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: A 532 ARG cc_start: 0.6402 (tpp-160) cc_final: 0.6081 (mmt180) REVERT: A 648 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8167 (ttpp) outliers start: 15 outliers final: 12 residues processed: 70 average time/residue: 0.0829 time to fit residues: 7.1030 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 : 0.086 ------------------------------------------------------------------------------- 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 198 ASP 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 597 THR 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: 20.0000 chunk 15 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4794 r_free = 0.4794 target = 0.262343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.206503 restraints weight = 4946.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.211781 restraints weight = 2941.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.215285 restraints weight = 2110.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.217268 restraints weight = 1718.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.218687 restraints weight = 1516.351| |-----------------------------------------------------------------------------| r_work (final): 0.4448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.4062 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= 0.146 Angle : 0.718 15.644 5929 Z= 0.315 Chirality : 0.042 0.220 691 Planarity : 0.004 0.049 718 Dihedral : 13.097 123.904 724 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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: 1.57 (0.34), residues: 555 helix: 1.86 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.47 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 246 TYR 0.020 0.001 TYR A 590 PHE 0.010 0.001 PHE A 73 TRP 0.005 0.001 TRP A 259 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 4343) covalent geometry : angle 0.65259 ( 5906) SS BOND : bond 0.00135 ( 7) SS BOND : angle 1.25161 ( 14) hydrogen bonds : bond 0.04304 ( 258) hydrogen bonds : angle 4.25178 ( 774) link_BETA1-4 : bond 0.00631 ( 1) link_BETA1-4 : angle 5.50366 ( 3) link_NAG-ASN : bond 0.01326 ( 2) link_NAG-ASN : angle 8.41637 ( 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 : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.6069 (OUTLIER) cc_final: 0.5711 (t0) REVERT: A 467 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: A 532 ARG cc_start: 0.6450 (tpp-160) cc_final: 0.6148 (mmt180) REVERT: A 648 LYS cc_start: 0.8410 (ttpt) cc_final: 0.7927 (tttm) outliers start: 14 outliers final: 11 residues processed: 71 average time/residue: 0.0779 time to fit residues: 6.8717 Evaluate side-chains 72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.138 ------------------------------------------------------------------------------- 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 198 ASP 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 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: 20.0000 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 2 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.263345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.207473 restraints weight = 5001.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.212739 restraints weight = 2946.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.216317 restraints weight = 2105.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.218350 restraints weight = 1708.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.219571 restraints weight = 1504.747| |-----------------------------------------------------------------------------| r_work (final): 0.4455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4159 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= 0.137 Angle : 0.705 14.397 5929 Z= 0.311 Chirality : 0.040 0.187 691 Planarity : 0.004 0.050 718 Dihedral : 12.355 108.676 724 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % 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: 1.61 (0.34), residues: 555 helix: 1.88 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.44 (0.40), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 526 TYR 0.020 0.001 TYR A 590 PHE 0.009 0.001 PHE A 73 TRP 0.005 0.001 TRP A 171 HIS 0.003 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4343) covalent geometry : angle 0.64746 ( 5906) SS BOND : bond 0.00103 ( 7) SS BOND : angle 1.15303 ( 14) hydrogen bonds : bond 0.04197 ( 258) hydrogen bonds : angle 4.20525 ( 774) link_BETA1-4 : bond 0.00853 ( 1) link_BETA1-4 : angle 5.04254 ( 3) link_NAG-ASN : bond 0.01212 ( 2) link_NAG-ASN : angle 7.92210 ( 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 72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASP cc_start: 0.6034 (OUTLIER) cc_final: 0.5730 (t0) REVERT: A 467 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: A 532 ARG cc_start: 0.6418 (tpp-160) cc_final: 0.6163 (mmt180) REVERT: A 580 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7184 (ttp-170) REVERT: A 648 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8081 (ttpp) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.0857 time to fit residues: 7.2666 Evaluate side-chains 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.137 ------------------------------------------------------------------------------- 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 198 ASP 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 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: 4.9990 chunk 14 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.0670 chunk 23 optimal weight: 0.0040 chunk 11 optimal weight: 20.0000 chunk 41 optimal weight: 6.9990 chunk 12 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 overall best weight: 0.2730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4837 r_free = 0.4837 target = 0.267281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.212085 restraints weight = 4908.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.217379 restraints weight = 2894.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.220958 restraints weight = 2071.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.222931 restraints weight = 1679.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.224328 restraints weight = 1483.067| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.4321 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= 0.122 Angle : 0.708 16.065 5929 Z= 0.313 Chirality : 0.041 0.211 691 Planarity : 0.004 0.046 718 Dihedral : 12.392 108.197 724 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.69 % Allowed : 24.21 % 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: 1.63 (0.34), residues: 555 helix: 1.92 (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 0.005 0.001 ARG A 181 TYR 0.019 0.001 TYR A 590 PHE 0.009 0.001 PHE A 175 TRP 0.008 0.001 TRP A 171 HIS 0.006 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4343) covalent geometry : angle 0.64219 ( 5906) SS BOND : bond 0.00063 ( 7) SS BOND : angle 1.01254 ( 14) hydrogen bonds : bond 0.04024 ( 258) hydrogen bonds : angle 4.11230 ( 774) link_BETA1-4 : bond 0.00344 ( 1) link_BETA1-4 : angle 5.10653 ( 3) link_NAG-ASN : bond 0.00988 ( 2) link_NAG-ASN : angle 8.57151 ( 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 76 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.6487 (mmt) cc_final: 0.6093 (mmt) REVERT: A 198 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5661 (t0) REVERT: A 267 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.5493 (tt) REVERT: A 467 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: A 532 ARG cc_start: 0.6307 (tpp-160) cc_final: 0.6047 (mmt180) REVERT: A 591 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.5535 (t80) REVERT: A 594 LEU cc_start: 0.6740 (tt) cc_final: 0.6431 (tp) REVERT: A 648 LYS cc_start: 0.8348 (ttpt) cc_final: 0.8055 (ttpp) outliers start: 11 outliers final: 7 residues processed: 73 average time/residue: 0.0754 time to fit residues: 6.8729 Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain A residue 340 MET 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 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: 0.8980 chunk 54 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4772 r_free = 0.4772 target = 0.259600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.207748 restraints weight = 4831.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.212587 restraints weight = 2909.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.215899 restraints weight = 2093.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.217745 restraints weight = 1698.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.218719 restraints weight = 1495.456| |-----------------------------------------------------------------------------| r_work (final): 0.4493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4353 Z= 0.139 Angle : 0.711 15.426 5929 Z= 0.316 Chirality : 0.041 0.203 691 Planarity : 0.004 0.047 718 Dihedral : 12.388 110.552 724 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.69 % Allowed : 23.72 % 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: 1.54 (0.35), residues: 555 helix: 1.79 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -0.47 (0.41), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 181 TYR 0.026 0.001 TYR A 590 PHE 0.008 0.001 PHE A 73 TRP 0.015 0.001 TRP A 254 HIS 0.004 0.001 HIS A 54 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4343) covalent geometry : angle 0.65087 ( 5906) SS BOND : bond 0.00097 ( 7) SS BOND : angle 1.04342 ( 14) hydrogen bonds : bond 0.04100 ( 258) hydrogen bonds : angle 4.17643 ( 774) link_BETA1-4 : bond 0.00963 ( 1) link_BETA1-4 : angle 4.69416 ( 3) link_NAG-ASN : bond 0.01316 ( 2) link_NAG-ASN : angle 8.34497 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 844.69 seconds wall clock time: 15 minutes 11.96 seconds (911.96 seconds total)