Starting phenix.real_space_refine on Wed Jul 23 20:42:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hnh_34913/07_2025/8hnh_34913.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hnh_34913/07_2025/8hnh_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2025/8hnh_34913.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2025/8hnh_34913.map" model { file = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2025/8hnh_34913.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hnh_34913/07_2025/8hnh_34913.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.041 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 1, 'HIS:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 10, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 4} 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: 3.26, per 1000 atoms: 0.77 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: 1.26 Conformation dependent library (CDL) restraints added in 524.2 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: 0.36 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: 1.06 Time building geometry restraints manager: 1.50 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: 0.690 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.600 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (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 TRP 0.019 0.002 TRP A 259 HIS 0.005 0.001 HIS A 555 PHE 0.020 0.002 PHE A 341 TYR 0.025 0.002 TYR A 590 ARG 0.003 0.000 ARG A 246 Details of bonding type rmsd link_NAG-ASN : bond 0.08868 ( 2) link_NAG-ASN : angle 14.70656 ( 6) link_BETA1-4 : bond 0.08095 ( 1) link_BETA1-4 : angle 18.44695 ( 3) hydrogen bonds : bond 0.24573 ( 258) hydrogen bonds : angle 7.90949 ( 774) SS BOND : bond 0.00398 ( 7) SS BOND : angle 0.84214 ( 14) covalent geometry : bond 0.00872 ( 4343) covalent geometry : angle 1.44444 ( 5906) *********************** 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 : 0.451 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: 0.1701 time to fit residues: 21.2715 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 : 0.404 ------------------------------------------------------------------------------- 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 47 optimal weight: 0.5980 chunk 42 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.1980 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.237116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.198039 restraints weight = 3992.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.198309 restraints weight = 3267.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.198912 restraints weight = 2727.068| |-----------------------------------------------------------------------------| r_work (final): 0.4272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4353 Z= 0.168 Angle : 0.809 15.867 5929 Z= 0.367 Chirality : 0.047 0.359 691 Planarity : 0.005 0.057 718 Dihedral : 17.101 169.135 733 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.93 % Allowed : 18.58 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.34), residues: 555 helix: 2.28 (0.26), residues: 351 sheet: None (None), residues: 0 loop : -0.43 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 171 HIS 0.002 0.001 HIS A 575 PHE 0.016 0.002 PHE A 73 TYR 0.018 0.002 TYR A 590 ARG 0.003 0.001 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01296 ( 2) link_NAG-ASN : angle 7.40389 ( 6) link_BETA1-4 : bond 0.01087 ( 1) link_BETA1-4 : angle 9.71661 ( 3) hydrogen bonds : bond 0.06306 ( 258) hydrogen bonds : angle 5.14002 ( 774) SS BOND : bond 0.00253 ( 7) SS BOND : angle 0.61835 ( 14) covalent geometry : bond 0.00351 ( 4343) covalent geometry : angle 0.74319 ( 5906) *********************** 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 78 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 648 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8433 (ttpp) outliers start: 12 outliers final: 7 residues processed: 73 average time/residue: 0.1745 time to fit residues: 15.9354 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 : 0.376 ------------------------------------------------------------------------------- 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 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 52 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4780 r_free = 0.4780 target = 0.259768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.207326 restraints weight = 4806.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.212380 restraints weight = 2864.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.215863 restraints weight = 2046.551| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 moved from start: 0.2949 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= 0.146 Angle : 0.754 18.577 5929 Z= 0.334 Chirality : 0.042 0.276 691 Planarity : 0.004 0.050 718 Dihedral : 15.448 168.785 728 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.93 % Allowed : 19.32 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.34), residues: 555 helix: 1.98 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 171 HIS 0.003 0.001 HIS A 54 PHE 0.014 0.001 PHE A 73 TYR 0.020 0.002 TYR A 590 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01520 ( 2) link_NAG-ASN : angle 9.68930 ( 6) link_BETA1-4 : bond 0.01113 ( 1) link_BETA1-4 : angle 7.89237 ( 3) hydrogen bonds : bond 0.05056 ( 258) hydrogen bonds : angle 4.63919 ( 774) SS BOND : bond 0.00195 ( 7) SS BOND : angle 0.68466 ( 14) covalent geometry : bond 0.00318 ( 4343) covalent geometry : angle 0.66495 ( 5906) *********************** 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 73 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8015 (mm) cc_final: 0.7681 (mm) REVERT: A 198 ASP cc_start: 0.6214 (OUTLIER) cc_final: 0.5902 (t0) REVERT: A 648 LYS cc_start: 0.8608 (ttpt) cc_final: 0.8249 (ttpp) outliers start: 12 outliers final: 6 residues processed: 69 average time/residue: 0.1800 time to fit residues: 15.7181 Evaluate side-chains 67 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 5 optimal weight: 0.9990 chunk 28 optimal weight: 0.0050 chunk 10 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- 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 = 0.4762 r_free = 0.4762 target = 0.258320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.205592 restraints weight = 4861.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.210673 restraints weight = 2889.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.214132 restraints weight = 2068.386| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4353 Z= 0.138 Angle : 0.714 15.249 5929 Z= 0.313 Chirality : 0.042 0.255 691 Planarity : 0.004 0.053 718 Dihedral : 14.935 168.974 724 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.44 % Allowed : 20.29 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.34), residues: 555 helix: 1.88 (0.26), residues: 360 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.003 0.001 HIS A 54 PHE 0.015 0.001 PHE A 386 TYR 0.020 0.001 TYR A 590 ARG 0.005 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01351 ( 2) link_NAG-ASN : angle 8.42254 ( 6) link_BETA1-4 : bond 0.01064 ( 1) link_BETA1-4 : angle 7.58609 ( 3) hydrogen bonds : bond 0.04659 ( 258) hydrogen bonds : angle 4.42012 ( 774) SS BOND : bond 0.00286 ( 7) SS BOND : angle 0.64330 ( 14) covalent geometry : bond 0.00310 ( 4343) covalent geometry : angle 0.63960 ( 5906) *********************** 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: 10 poor density : 67 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8060 (mm) cc_final: 0.7857 (mm) REVERT: A 118 MET cc_start: 0.6575 (mpp) cc_final: 0.6311 (mpp) REVERT: A 198 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.5942 (t0) REVERT: A 591 PHE cc_start: 0.7189 (OUTLIER) cc_final: 0.5115 (t80) REVERT: A 648 LYS cc_start: 0.8530 (ttpt) cc_final: 0.8178 (ttpp) outliers start: 10 outliers final: 7 residues processed: 75 average time/residue: 0.1664 time to fit residues: 15.7350 Evaluate side-chains 70 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 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 640 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4762 r_free = 0.4762 target = 0.258165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.205180 restraints weight = 4881.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.210241 restraints weight = 2898.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.213697 restraints weight = 2069.162| |-----------------------------------------------------------------------------| r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3555 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= 0.141 Angle : 0.729 13.725 5929 Z= 0.323 Chirality : 0.042 0.231 691 Planarity : 0.004 0.049 718 Dihedral : 14.605 156.063 724 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 4.40 % Allowed : 19.32 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.34), residues: 555 helix: 1.85 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.53 (0.39), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.004 0.001 HIS A 54 PHE 0.010 0.001 PHE A 73 TYR 0.022 0.001 TYR A 590 ARG 0.005 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01079 ( 2) link_NAG-ASN : angle 7.82638 ( 6) link_BETA1-4 : bond 0.01106 ( 1) link_BETA1-4 : angle 6.77488 ( 3) hydrogen bonds : bond 0.04509 ( 258) hydrogen bonds : angle 4.40161 ( 774) SS BOND : bond 0.00115 ( 7) SS BOND : angle 2.26124 ( 14) covalent geometry : bond 0.00322 ( 4343) covalent geometry : angle 0.66025 ( 5906) *********************** 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: 18 poor density : 61 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8120 (mm) cc_final: 0.7818 (mm) REVERT: A 118 MET cc_start: 0.6671 (mpp) cc_final: 0.6354 (mpp) REVERT: A 198 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.5884 (t0) REVERT: A 267 LEU cc_start: 0.6185 (OUTLIER) cc_final: 0.5448 (tt) REVERT: A 591 PHE cc_start: 0.7249 (OUTLIER) cc_final: 0.5163 (t80) REVERT: A 648 LYS cc_start: 0.8500 (ttpt) cc_final: 0.8157 (ttpp) outliers start: 18 outliers final: 11 residues processed: 75 average time/residue: 0.1844 time to fit residues: 17.4231 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 : 0.450 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.9990 chunk 42 optimal weight: 20.0000 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 52 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 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 = 0.4735 r_free = 0.4735 target = 0.254309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.211635 restraints weight = 4130.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.211801 restraints weight = 4319.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.214002 restraints weight = 3702.725| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3714 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= 0.140 Angle : 0.718 17.550 5929 Z= 0.315 Chirality : 0.041 0.218 691 Planarity : 0.004 0.049 718 Dihedral : 14.175 153.047 724 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.40 % Allowed : 19.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.34), residues: 555 helix: 1.85 (0.27), residues: 358 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 254 HIS 0.004 0.001 HIS A 54 PHE 0.009 0.001 PHE A 73 TYR 0.031 0.001 TYR A 590 ARG 0.004 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01007 ( 2) link_NAG-ASN : angle 9.25962 ( 6) link_BETA1-4 : bond 0.00645 ( 1) link_BETA1-4 : angle 5.70936 ( 3) hydrogen bonds : bond 0.04403 ( 258) hydrogen bonds : angle 4.32263 ( 774) SS BOND : bond 0.00114 ( 7) SS BOND : angle 1.40803 ( 14) covalent geometry : bond 0.00322 ( 4343) covalent geometry : angle 0.63991 ( 5906) *********************** 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 79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7632 (ttp80) REVERT: A 198 ASP cc_start: 0.5920 (OUTLIER) cc_final: 0.5637 (t0) REVERT: A 267 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.5730 (tt) REVERT: A 467 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: A 532 ARG cc_start: 0.6463 (tpp-160) cc_final: 0.6148 (mmt180) REVERT: A 648 LYS cc_start: 0.8515 (ttpt) cc_final: 0.8195 (ttpp) outliers start: 18 outliers final: 12 residues processed: 75 average time/residue: 0.1661 time to fit residues: 15.7157 Evaluate side-chains 74 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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 8 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4785 r_free = 0.4785 target = 0.261325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.204666 restraints weight = 4973.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.209882 restraints weight = 2967.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.213262 restraints weight = 2139.561| |-----------------------------------------------------------------------------| r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4353 Z= 0.150 Angle : 0.725 13.940 5929 Z= 0.320 Chirality : 0.042 0.227 691 Planarity : 0.004 0.050 718 Dihedral : 13.673 140.514 724 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.91 % Allowed : 22.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.34), residues: 555 helix: 1.76 (0.27), residues: 356 sheet: None (None), residues: 0 loop : -0.43 (0.40), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 254 HIS 0.005 0.001 HIS A 54 PHE 0.018 0.001 PHE A 386 TYR 0.021 0.001 TYR A 590 ARG 0.003 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01091 ( 2) link_NAG-ASN : angle 7.68510 ( 6) link_BETA1-4 : bond 0.00878 ( 1) link_BETA1-4 : angle 5.61705 ( 3) hydrogen bonds : bond 0.04465 ( 258) hydrogen bonds : angle 4.33945 ( 774) SS BOND : bond 0.00141 ( 7) SS BOND : angle 1.35023 ( 14) covalent geometry : bond 0.00352 ( 4343) covalent geometry : angle 0.66854 ( 5906) *********************** 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 76 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6864 (OUTLIER) cc_final: 0.6078 (mpp) REVERT: A 198 ASP cc_start: 0.6146 (OUTLIER) cc_final: 0.5784 (t0) REVERT: A 467 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: A 532 ARG cc_start: 0.6475 (tpp-160) cc_final: 0.6167 (mmt180) REVERT: A 648 LYS cc_start: 0.8423 (ttpt) cc_final: 0.8109 (ttpp) outliers start: 16 outliers final: 12 residues processed: 72 average time/residue: 0.1953 time to fit residues: 17.6774 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 : 0.395 ------------------------------------------------------------------------------- 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 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 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.2980 chunk 23 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4806 r_free = 0.4806 target = 0.264001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208074 restraints weight = 4906.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.213359 restraints weight = 2910.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.216837 restraints weight = 2081.609| |-----------------------------------------------------------------------------| r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 0.036 4353 Z= 0.132 Angle : 0.719 18.931 5929 Z= 0.312 Chirality : 0.041 0.252 691 Planarity : 0.004 0.048 718 Dihedral : 12.585 108.241 724 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.18 % Allowed : 23.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.35), residues: 555 helix: 1.87 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.38 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.004 0.001 HIS A 54 PHE 0.009 0.001 PHE A 73 TYR 0.021 0.001 TYR A 590 ARG 0.006 0.001 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01535 ( 2) link_NAG-ASN : angle 9.63738 ( 6) link_BETA1-4 : bond 0.00592 ( 1) link_BETA1-4 : angle 5.63758 ( 3) hydrogen bonds : bond 0.04192 ( 258) hydrogen bonds : angle 4.20949 ( 774) SS BOND : bond 0.00095 ( 7) SS BOND : angle 1.12800 ( 14) covalent geometry : bond 0.00292 ( 4343) covalent geometry : angle 0.63638 ( 5906) *********************** 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 71 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6501 (mpp) REVERT: A 181 ARG cc_start: 0.7765 (mtp85) cc_final: 0.7423 (ttp80) REVERT: A 198 ASP cc_start: 0.6030 (OUTLIER) cc_final: 0.5745 (t0) REVERT: A 467 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: A 532 ARG cc_start: 0.6427 (tpp-160) cc_final: 0.6166 (mmt180) REVERT: A 648 LYS cc_start: 0.8369 (ttpt) cc_final: 0.7886 (tttm) outliers start: 13 outliers final: 9 residues processed: 68 average time/residue: 0.1925 time to fit residues: 16.4002 Evaluate side-chains 68 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 118 MET 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 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 39 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 53 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.4817 r_free = 0.4817 target = 0.265494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.209337 restraints weight = 4953.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.214688 restraints weight = 2924.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.218289 restraints weight = 2094.003| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.4088 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 : 0.710 17.998 5929 Z= 0.310 Chirality : 0.041 0.227 691 Planarity : 0.004 0.047 718 Dihedral : 12.392 110.655 724 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.44 % Allowed : 24.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.35), residues: 555 helix: 1.87 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.34 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.003 0.001 HIS A 54 PHE 0.019 0.001 PHE A 386 TYR 0.019 0.001 TYR A 590 ARG 0.005 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01640 ( 2) link_NAG-ASN : angle 9.42360 ( 6) link_BETA1-4 : bond 0.00800 ( 1) link_BETA1-4 : angle 4.97301 ( 3) hydrogen bonds : bond 0.04086 ( 258) hydrogen bonds : angle 4.17751 ( 774) SS BOND : bond 0.00123 ( 7) SS BOND : angle 1.02542 ( 14) covalent geometry : bond 0.00274 ( 4343) covalent geometry : angle 0.63339 ( 5906) *********************** 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 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6886 (OUTLIER) cc_final: 0.6517 (mpp) REVERT: A 198 ASP cc_start: 0.5932 (OUTLIER) cc_final: 0.5666 (t0) REVERT: A 467 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: A 532 ARG cc_start: 0.6381 (tpp-160) cc_final: 0.6137 (mmt180) REVERT: A 580 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7190 (ttp-170) REVERT: A 591 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.5386 (t80) REVERT: A 648 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8046 (ttpp) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.1911 time to fit residues: 15.6610 Evaluate side-chains 66 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 118 MET 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 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 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 11 optimal weight: 0.0170 chunk 23 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.4784 r_free = 0.4784 target = 0.261509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.209715 restraints weight = 4808.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.214633 restraints weight = 2861.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.217978 restraints weight = 2052.247| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.4203 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= 0.123 Angle : 0.705 17.847 5929 Z= 0.308 Chirality : 0.041 0.214 691 Planarity : 0.004 0.046 718 Dihedral : 12.376 111.218 724 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.35), residues: 555 helix: 1.93 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.27 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 171 HIS 0.003 0.001 HIS A 54 PHE 0.008 0.001 PHE A 73 TYR 0.026 0.001 TYR A 590 ARG 0.005 0.000 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01455 ( 2) link_NAG-ASN : angle 9.23632 ( 6) link_BETA1-4 : bond 0.00773 ( 1) link_BETA1-4 : angle 4.74229 ( 3) hydrogen bonds : bond 0.03965 ( 258) hydrogen bonds : angle 4.11620 ( 774) SS BOND : bond 0.00064 ( 7) SS BOND : angle 0.96481 ( 14) covalent geometry : bond 0.00265 ( 4343) covalent geometry : angle 0.63111 ( 5906) ********************** 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 69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 MET cc_start: 0.6865 (OUTLIER) cc_final: 0.6493 (mpp) REVERT: A 198 ASP cc_start: 0.5852 (OUTLIER) cc_final: 0.5589 (t0) REVERT: A 267 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5429 (tt) REVERT: A 365 GLN cc_start: 0.7583 (mm110) cc_final: 0.7113 (mm-40) REVERT: A 467 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: A 532 ARG cc_start: 0.6351 (tpp-160) cc_final: 0.6103 (mmt180) REVERT: A 580 ARG cc_start: 0.7588 (mtp-110) cc_final: 0.6915 (mtm-85) REVERT: A 648 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7951 (ttpp) outliers start: 11 outliers final: 7 residues processed: 66 average time/residue: 0.1890 time to fit residues: 15.5494 Evaluate side-chains 67 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 PHE Chi-restraints excluded: chain A residue 118 MET 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 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 8 optimal weight: 0.6980 chunk 40 optimal weight: 0.0270 chunk 11 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 31 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.4773 r_free = 0.4773 target = 0.259961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.208168 restraints weight = 4863.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.212763 restraints weight = 2896.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.216231 restraints weight = 2084.083| |-----------------------------------------------------------------------------| r_work (final): 0.4453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4353 Z= 0.131 Angle : 0.700 17.305 5929 Z= 0.307 Chirality : 0.041 0.211 691 Planarity : 0.004 0.047 718 Dihedral : 12.388 113.069 724 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.42 % Allowed : 23.96 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.35), residues: 555 helix: 1.92 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -0.22 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 171 HIS 0.004 0.001 HIS A 54 PHE 0.011 0.001 PHE A 386 TYR 0.028 0.001 TYR A 590 ARG 0.006 0.001 ARG A 181 Details of bonding type rmsd link_NAG-ASN : bond 0.01401 ( 2) link_NAG-ASN : angle 9.03839 ( 6) link_BETA1-4 : bond 0.00856 ( 1) link_BETA1-4 : angle 4.51180 ( 3) hydrogen bonds : bond 0.04025 ( 258) hydrogen bonds : angle 4.14425 ( 774) SS BOND : bond 0.00086 ( 7) SS BOND : angle 0.94105 ( 14) covalent geometry : bond 0.00294 ( 4343) covalent geometry : angle 0.62918 ( 5906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1686.70 seconds wall clock time: 30 minutes 1.15 seconds (1801.15 seconds total)