Starting phenix.real_space_refine on Tue Mar 3 15:47:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de3_27383/03_2026/8de3_27383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de3_27383/03_2026/8de3_27383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8de3_27383/03_2026/8de3_27383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de3_27383/03_2026/8de3_27383.map" model { file = "/net/cci-nas-00/data/ceres_data/8de3_27383/03_2026/8de3_27383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de3_27383/03_2026/8de3_27383.cif" } resolution = 3.3 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= 0.020 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: 6 Type Number sf(0) Gaussians S 35 5.16 5 Cl 1 4.86 5 Na 2 4.78 5 C 4100 2.51 5 N 957 2.21 5 O 1104 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 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: 6199 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4298 Classifications: {'peptide': 539} Link IDs: {'PTRANS': 23, 'TRANS': 515} Chain breaks: 1 Chain: "B" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 913 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "C" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 830 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 103} Chain: "D" 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: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 130 Unusual residues: {' CL': 1, ' NA': 2, 'COC': 1, 'LMT': 1, 'Y01': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 1.34, per 1000 atoms: 0.22 Number of scatterers: 6199 At special positions: 0 Unit cell: (75.621, 75.621, 116.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 35 16.00 Na 2 11.00 O 1104 8.00 N 957 7.00 C 4100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 112 " 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 D 1 " - " NAG D 2 " NAG-ASN " NAG D 1 " - " ASN A 245 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 224.0 milliseconds 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 7 sheets defined 58.3% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.772A pdb=" N PHE A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.532A pdb=" N VAL A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 150 through 153 removed outlier: 3.967A pdb=" N ALA A 153 " --> pdb=" O GLY A 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 153' Processing helix chain 'A' and resid 154 through 166 Processing helix chain 'A' and resid 166 through 181 removed outlier: 3.669A pdb=" N HIS A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 193 through 196 removed outlier: 3.581A pdb=" N LYS A 196 " --> pdb=" O PRO A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 193 through 196' Processing helix chain 'A' and resid 197 through 227 removed outlier: 3.929A pdb=" N TYR A 212 " --> pdb=" O TYR A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 289 through 307 Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.811A pdb=" N VAL A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 338 removed outlier: 3.626A pdb=" N THR A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 350 removed outlier: 3.672A pdb=" N GLY A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.822A pdb=" N LEU A 358 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 removed outlier: 4.213A pdb=" N TRP A 363 " --> pdb=" O GLU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 3.713A pdb=" N TYR A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 427 removed outlier: 3.659A pdb=" N ASP A 397 " --> pdb=" O ASN A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 454 removed outlier: 4.258A pdb=" N LEU A 443 " --> pdb=" O GLY A 439 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHE A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA A 448 " --> pdb=" O PHE A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 490 removed outlier: 3.599A pdb=" N SER A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 518 removed outlier: 4.420A pdb=" N TRP A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ILE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR A 517 " --> pdb=" O GLY A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 531 removed outlier: 4.199A pdb=" N VAL A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 552 Processing helix chain 'A' and resid 554 through 567 Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.844A pdb=" N VAL A 579 " --> pdb=" O ARG A 575 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 595 Processing helix chain 'A' and resid 608 through 624 removed outlier: 3.696A pdb=" N ILE A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER A 622 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE A 623 " --> pdb=" O GLY A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 Processing helix chain 'A' and resid 640 through 650 removed outlier: 4.425A pdb=" N ILE A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL A 646 " --> pdb=" O LYS A 642 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY A 648 " --> pdb=" O ARG A 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 51 removed outlier: 3.811A pdb=" N SER B 51 " --> pdb=" O PHE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 110 removed outlier: 3.613A pdb=" N ASP B 109 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.021A pdb=" N THR C 107 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 601 through 602 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 25 removed outlier: 3.549A pdb=" N GLN B 22 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 44 " --> pdb=" O GLN B 22 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA B 35 " --> pdb=" O SER B 104 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER B 104 " --> pdb=" O ALA B 35 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.587A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N TYR B 129 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 78 removed outlier: 6.587A pdb=" N TRP B 55 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG B 69 " --> pdb=" O MET B 53 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B 53 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 27 removed outlier: 3.822A pdb=" N SER C 42 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 95 " --> pdb=" O CYS C 43 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR C 94 " --> pdb=" O SER C 91 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER C 91 " --> pdb=" O TYR C 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.857A pdb=" N LEU C 31 " --> pdb=" O GLU C 129 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 removed outlier: 6.871A pdb=" N TRP C 59 " --> pdb=" O LEU C 71 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TYR C 73 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N LEU C 57 " --> pdb=" O TYR C 73 " (cutoff:3.500A) 351 hydrogen bonds defined for protein. 993 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: 1.04 Time building geometry restraints manager: 0.85 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: 926 1.31 - 1.44: 1934 1.44 - 1.56: 3453 1.56 - 1.69: 20 1.69 - 1.81: 53 Bond restraints: 6386 Sorted by residual: bond pdb=" CAI Y01 A1006 " pdb=" CAZ Y01 A1006 " ideal model delta sigma weight residual 1.332 1.557 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" CAI Y01 A1005 " pdb=" CAZ Y01 A1005 " ideal model delta sigma weight residual 1.332 1.556 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" CAU Y01 A1005 " pdb=" CBI Y01 A1005 " ideal model delta sigma weight residual 1.530 1.719 -0.189 2.00e-02 2.50e+03 8.90e+01 bond pdb=" CAU Y01 A1006 " pdb=" CBI Y01 A1006 " ideal model delta sigma weight residual 1.530 1.717 -0.187 2.00e-02 2.50e+03 8.77e+01 bond pdb=" CAP Y01 A1006 " pdb=" CBE Y01 A1006 " ideal model delta sigma weight residual 1.553 1.385 0.168 2.00e-02 2.50e+03 7.06e+01 ... (remaining 6381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 8589 2.45 - 4.90: 87 4.90 - 7.35: 14 7.35 - 9.80: 10 9.80 - 12.25: 5 Bond angle restraints: 8705 Sorted by residual: angle pdb=" CAK Y01 A1005 " pdb=" CAI Y01 A1005 " pdb=" CAZ Y01 A1005 " ideal model delta sigma weight residual 124.96 112.71 12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" CAK Y01 A1006 " pdb=" CAI Y01 A1006 " pdb=" CAZ Y01 A1006 " ideal model delta sigma weight residual 124.96 113.38 11.58 3.00e+00 1.11e-01 1.49e+01 angle pdb=" CAI Y01 A1005 " pdb=" CAZ Y01 A1005 " pdb=" CBH Y01 A1005 " ideal model delta sigma weight residual 123.00 112.65 10.35 3.00e+00 1.11e-01 1.19e+01 angle pdb=" CAI Y01 A1006 " pdb=" CAZ Y01 A1006 " pdb=" CBH Y01 A1006 " ideal model delta sigma weight residual 123.00 113.08 9.92 3.00e+00 1.11e-01 1.09e+01 angle pdb=" C2 LMT A1007 " pdb=" C3 LMT A1007 " pdb=" C4 LMT A1007 " ideal model delta sigma weight residual 117.09 107.28 9.81 3.00e+00 1.11e-01 1.07e+01 ... (remaining 8700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3226 17.36 - 34.73: 428 34.73 - 52.09: 135 52.09 - 69.45: 25 69.45 - 86.82: 6 Dihedral angle restraints: 3820 sinusoidal: 1622 harmonic: 2198 Sorted by residual: dihedral pdb=" CB CYS C 43 " pdb=" SG CYS C 43 " pdb=" SG CYS C 112 " pdb=" CB CYS C 112 " ideal model delta sinusoidal sigma weight residual 93.00 132.06 -39.06 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CB CYS A 237 " pdb=" SG CYS A 237 " pdb=" SG CYS A 246 " pdb=" CB CYS A 246 " ideal model delta sinusoidal sigma weight residual 93.00 130.23 -37.23 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA GLU C 129 " pdb=" C GLU C 129 " pdb=" N ILE C 130 " pdb=" CA ILE C 130 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 ... (remaining 3817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 936 0.097 - 0.193: 29 0.193 - 0.290: 5 0.290 - 0.387: 0 0.387 - 0.483: 2 Chirality restraints: 972 Sorted by residual: chirality pdb=" CBG Y01 A1006 " pdb=" CAQ Y01 A1006 " pdb=" CBD Y01 A1006 " pdb=" CBI Y01 A1006 " both_signs ideal model delta sigma weight residual False -2.33 -2.82 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CBG Y01 A1005 " pdb=" CAQ Y01 A1005 " pdb=" CBD Y01 A1005 " pdb=" CBI Y01 A1005 " both_signs ideal model delta sigma weight residual False -2.33 -2.81 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CBI Y01 A1006 " pdb=" CAU Y01 A1006 " pdb=" CBE Y01 A1006 " pdb=" CBG Y01 A1006 " both_signs ideal model delta sigma weight residual False 2.94 2.70 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 969 not shown) Planarity restraints: 1054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A 351 " -0.045 5.00e-02 4.00e+02 6.87e-02 7.55e+00 pdb=" N PRO A 352 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 352 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 352 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 348 " 0.007 2.00e-02 2.50e+03 9.13e-03 1.46e+00 pdb=" CG PHE A 348 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 348 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 348 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 348 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 348 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 348 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 477 " -0.007 2.00e-02 2.50e+03 8.73e-03 1.33e+00 pdb=" CG PHE A 477 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE A 477 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 477 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 477 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 477 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 477 " 0.000 2.00e-02 2.50e+03 ... (remaining 1051 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 245 2.72 - 3.27: 6105 3.27 - 3.81: 10601 3.81 - 4.36: 12394 4.36 - 4.90: 21440 Nonbonded interactions: 50785 Sorted by model distance: nonbonded pdb=" OD1 ASP A 135 " pdb=" OH TYR A 213 " model vdw 2.178 3.040 nonbonded pdb=" O SER A 596 " pdb=" O6' LMT A1007 " model vdw 2.178 3.040 nonbonded pdb=" O ASN A 182 " pdb=" OG SER A 386 " model vdw 2.227 3.040 nonbonded pdb=" O CYS A 184 " pdb=" NE1 TRP A 188 " model vdw 2.290 3.120 nonbonded pdb=" OG1 THR A 215 " pdb=" OG1 THR A 517 " model vdw 2.295 3.040 ... (remaining 50780 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.360 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.090 Find NCS groups from input model: 0.030 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 : 0.008 0.225 6391 Z= 0.425 Angle : 0.688 12.253 8717 Z= 0.283 Chirality : 0.047 0.483 972 Planarity : 0.003 0.069 1053 Dihedral : 17.064 86.818 2415 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.16 % Allowed : 29.97 % Favored : 69.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.95 (0.32), residues: 759 helix: 1.95 (0.27), residues: 371 sheet: 0.40 (0.61), residues: 87 loop : -1.01 (0.37), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 38 TYR 0.008 0.001 TYR A 212 PHE 0.021 0.001 PHE A 348 TRP 0.009 0.001 TRP A 234 HIS 0.001 0.000 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00848 ( 6386) covalent geometry : angle 0.68725 ( 8705) SS BOND : bond 0.00078 ( 3) SS BOND : angle 0.17621 ( 6) hydrogen bonds : bond 0.17141 ( 340) hydrogen bonds : angle 5.95978 ( 993) link_BETA1-4 : bond 0.00290 ( 1) link_BETA1-4 : angle 0.86513 ( 3) link_NAG-ASN : bond 0.00711 ( 1) link_NAG-ASN : angle 1.72909 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.157 Fit side-chains REVERT: A 297 MET cc_start: 0.7686 (tmm) cc_final: 0.5479 (mtt) REVERT: C 78 GLN cc_start: 0.7121 (mt0) cc_final: 0.6910 (mt0) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.0601 time to fit residues: 6.3140 Evaluate side-chains 69 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 88 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.0970 chunk 74 optimal weight: 0.9990 overall best weight: 0.3178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** 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 = 0.4338 r_free = 0.4338 target = 0.196754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.174451 restraints weight = 6632.346| |-----------------------------------------------------------------------------| r_work (start): 0.4116 rms_B_bonded: 1.75 r_work: 0.3916 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6391 Z= 0.113 Angle : 0.506 6.368 8717 Z= 0.254 Chirality : 0.039 0.215 972 Planarity : 0.004 0.057 1053 Dihedral : 8.378 59.347 1106 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.71 % Allowed : 28.26 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 1.10 (0.32), residues: 759 helix: 1.87 (0.26), residues: 371 sheet: 0.56 (0.55), residues: 114 loop : -0.78 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 644 TYR 0.011 0.001 TYR A 212 PHE 0.022 0.001 PHE A 477 TRP 0.009 0.001 TRP B 66 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 6386) covalent geometry : angle 0.50378 ( 8705) SS BOND : bond 0.00395 ( 3) SS BOND : angle 0.89241 ( 6) hydrogen bonds : bond 0.03148 ( 340) hydrogen bonds : angle 4.41627 ( 993) link_BETA1-4 : bond 0.00542 ( 1) link_BETA1-4 : angle 1.13127 ( 3) link_NAG-ASN : bond 0.00364 ( 1) link_NAG-ASN : angle 2.22932 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.225 Fit side-chains REVERT: A 297 MET cc_start: 0.7680 (tmm) cc_final: 0.5326 (mtt) REVERT: A 471 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8005 (mp) outliers start: 11 outliers final: 5 residues processed: 84 average time/residue: 0.0561 time to fit residues: 7.0896 Evaluate side-chains 78 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 72 optimal weight: 0.0570 chunk 6 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.187153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164070 restraints weight = 6598.113| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.46 r_work: 0.3764 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6391 Z= 0.176 Angle : 0.577 6.663 8717 Z= 0.291 Chirality : 0.043 0.343 972 Planarity : 0.004 0.046 1053 Dihedral : 7.724 59.596 1105 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.04 % Allowed : 27.17 % Favored : 68.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.56 (0.32), residues: 759 helix: 1.29 (0.26), residues: 372 sheet: 0.63 (0.55), residues: 114 loop : -1.01 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 47 TYR 0.021 0.002 TYR A 212 PHE 0.032 0.002 PHE A 477 TRP 0.012 0.001 TRP A 574 HIS 0.001 0.001 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6386) covalent geometry : angle 0.56837 ( 8705) SS BOND : bond 0.00485 ( 3) SS BOND : angle 1.13322 ( 6) hydrogen bonds : bond 0.04060 ( 340) hydrogen bonds : angle 4.56941 ( 993) link_BETA1-4 : bond 0.01991 ( 1) link_BETA1-4 : angle 1.94454 ( 3) link_NAG-ASN : bond 0.00412 ( 1) link_NAG-ASN : angle 4.95386 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 71 time to evaluate : 0.223 Fit side-chains REVERT: A 297 MET cc_start: 0.7831 (tmm) cc_final: 0.5409 (mtt) REVERT: A 471 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7981 (mp) outliers start: 26 outliers final: 13 residues processed: 90 average time/residue: 0.0580 time to fit residues: 7.7354 Evaluate side-chains 82 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 103 SER Chi-restraints excluded: chain C residue 24 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.0670 chunk 42 optimal weight: 0.8980 chunk 59 optimal weight: 0.0370 chunk 17 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 55 optimal weight: 0.0060 chunk 27 optimal weight: 0.2980 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 overall best weight: 0.2012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** 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 = 0.4257 r_free = 0.4257 target = 0.187994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.165244 restraints weight = 6561.123| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.48 r_work: 0.3819 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6391 Z= 0.099 Angle : 0.484 5.987 8717 Z= 0.246 Chirality : 0.039 0.300 972 Planarity : 0.003 0.039 1053 Dihedral : 7.483 58.555 1105 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.64 % Allowed : 29.50 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.86 (0.32), residues: 759 helix: 1.61 (0.26), residues: 372 sheet: 0.62 (0.54), residues: 114 loop : -0.89 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 38 TYR 0.009 0.001 TYR A 387 PHE 0.012 0.001 PHE A 477 TRP 0.012 0.001 TRP A 234 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 6386) covalent geometry : angle 0.47760 ( 8705) SS BOND : bond 0.00333 ( 3) SS BOND : angle 0.76458 ( 6) hydrogen bonds : bond 0.03178 ( 340) hydrogen bonds : angle 4.31499 ( 993) link_BETA1-4 : bond 0.00271 ( 1) link_BETA1-4 : angle 1.05000 ( 3) link_NAG-ASN : bond 0.00973 ( 1) link_NAG-ASN : angle 4.13294 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 69 time to evaluate : 0.225 Fit side-chains REVERT: A 297 MET cc_start: 0.7847 (tmm) cc_final: 0.5408 (mtt) REVERT: A 407 MET cc_start: 0.6024 (ptp) cc_final: 0.5786 (tmm) REVERT: A 420 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6521 (mp) REVERT: A 471 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7996 (mp) outliers start: 17 outliers final: 11 residues processed: 84 average time/residue: 0.0544 time to fit residues: 6.7869 Evaluate side-chains 79 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 62 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 65 optimal weight: 0.0970 chunk 3 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 8.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** 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 = 0.4235 r_free = 0.4235 target = 0.185508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.161686 restraints weight = 6705.085| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.45 r_work: 0.3764 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3621 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6391 Z= 0.175 Angle : 0.555 6.343 8717 Z= 0.283 Chirality : 0.042 0.353 972 Planarity : 0.004 0.035 1053 Dihedral : 7.565 57.649 1105 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.97 % Allowed : 27.17 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.55 (0.32), residues: 759 helix: 1.26 (0.26), residues: 373 sheet: 0.62 (0.55), residues: 114 loop : -0.97 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 644 TYR 0.017 0.002 TYR A 212 PHE 0.024 0.002 PHE A 477 TRP 0.009 0.001 TRP A 574 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 6386) covalent geometry : angle 0.54538 ( 8705) SS BOND : bond 0.00290 ( 3) SS BOND : angle 1.62259 ( 6) hydrogen bonds : bond 0.03742 ( 340) hydrogen bonds : angle 4.52708 ( 993) link_BETA1-4 : bond 0.00421 ( 1) link_BETA1-4 : angle 0.97559 ( 3) link_NAG-ASN : bond 0.00142 ( 1) link_NAG-ASN : angle 5.05170 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.179 Fit side-chains REVERT: A 297 MET cc_start: 0.7920 (tmm) cc_final: 0.5457 (mtt) REVERT: A 420 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6662 (mp) REVERT: A 471 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8161 (mp) REVERT: A 605 TYR cc_start: 0.7127 (t80) cc_final: 0.6643 (t80) outliers start: 32 outliers final: 22 residues processed: 96 average time/residue: 0.0517 time to fit residues: 7.4579 Evaluate side-chains 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 63 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 65 optimal weight: 0.0030 chunk 37 optimal weight: 0.3980 chunk 67 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.0370 chunk 66 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 overall best weight: 0.3268 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** 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 = 0.4225 r_free = 0.4225 target = 0.185494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161973 restraints weight = 6626.965| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.51 r_work: 0.3773 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6391 Z= 0.112 Angle : 0.505 6.365 8717 Z= 0.256 Chirality : 0.040 0.381 972 Planarity : 0.003 0.031 1053 Dihedral : 7.333 57.862 1105 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 5.12 % Allowed : 26.86 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.74 (0.32), residues: 759 helix: 1.44 (0.26), residues: 373 sheet: 0.58 (0.54), residues: 114 loop : -0.85 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 344 TYR 0.018 0.001 TYR A 387 PHE 0.013 0.001 PHE A 603 TRP 0.013 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6386) covalent geometry : angle 0.49668 ( 8705) SS BOND : bond 0.00291 ( 3) SS BOND : angle 1.15327 ( 6) hydrogen bonds : bond 0.03291 ( 340) hydrogen bonds : angle 4.35405 ( 993) link_BETA1-4 : bond 0.00662 ( 1) link_BETA1-4 : angle 1.09544 ( 3) link_NAG-ASN : bond 0.00262 ( 1) link_NAG-ASN : angle 4.46709 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 66 time to evaluate : 0.220 Fit side-chains REVERT: A 297 MET cc_start: 0.7852 (tmm) cc_final: 0.5423 (mtt) REVERT: A 407 MET cc_start: 0.5945 (ptp) cc_final: 0.5733 (tmm) REVERT: A 420 LEU cc_start: 0.7186 (OUTLIER) cc_final: 0.6594 (mp) REVERT: A 447 TYR cc_start: 0.7555 (OUTLIER) cc_final: 0.6556 (m-80) REVERT: A 471 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8112 (mp) outliers start: 33 outliers final: 23 residues processed: 96 average time/residue: 0.0538 time to fit residues: 7.7998 Evaluate side-chains 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 32 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 11 optimal weight: 0.0020 chunk 72 optimal weight: 0.9980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** 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 = 0.4245 r_free = 0.4245 target = 0.186731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.163091 restraints weight = 6612.905| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.51 r_work: 0.3781 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6391 Z= 0.134 Angle : 0.525 6.674 8717 Z= 0.267 Chirality : 0.040 0.332 972 Planarity : 0.003 0.029 1053 Dihedral : 7.081 54.767 1105 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 5.12 % Allowed : 27.17 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.66 (0.32), residues: 759 helix: 1.37 (0.26), residues: 373 sheet: 0.55 (0.54), residues: 114 loop : -0.88 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 69 TYR 0.019 0.001 TYR A 387 PHE 0.022 0.001 PHE A 477 TRP 0.012 0.001 TRP A 234 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6386) covalent geometry : angle 0.51780 ( 8705) SS BOND : bond 0.00358 ( 3) SS BOND : angle 1.26179 ( 6) hydrogen bonds : bond 0.03441 ( 340) hydrogen bonds : angle 4.42338 ( 993) link_BETA1-4 : bond 0.00474 ( 1) link_BETA1-4 : angle 0.87234 ( 3) link_NAG-ASN : bond 0.00401 ( 1) link_NAG-ASN : angle 4.49023 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.262 Fit side-chains REVERT: A 188 TRP cc_start: 0.7431 (m100) cc_final: 0.7094 (m100) REVERT: A 297 MET cc_start: 0.7871 (tmm) cc_final: 0.5411 (mtt) REVERT: A 420 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6627 (mp) REVERT: A 447 TYR cc_start: 0.7597 (OUTLIER) cc_final: 0.6633 (m-80) REVERT: A 471 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8187 (mp) outliers start: 33 outliers final: 26 residues processed: 94 average time/residue: 0.0534 time to fit residues: 7.5577 Evaluate side-chains 92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 15 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.2980 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 chunk 39 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 0.0370 chunk 50 optimal weight: 0.4980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.184281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.160674 restraints weight = 6715.963| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.92 r_work: 0.3763 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6391 Z= 0.122 Angle : 0.518 6.939 8717 Z= 0.262 Chirality : 0.040 0.371 972 Planarity : 0.003 0.029 1053 Dihedral : 6.917 52.117 1105 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.12 % Allowed : 27.02 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.69 (0.32), residues: 759 helix: 1.38 (0.26), residues: 375 sheet: 0.54 (0.53), residues: 114 loop : -0.85 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 69 TYR 0.018 0.001 TYR A 387 PHE 0.026 0.001 PHE A 348 TRP 0.014 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 6386) covalent geometry : angle 0.51059 ( 8705) SS BOND : bond 0.00322 ( 3) SS BOND : angle 1.11216 ( 6) hydrogen bonds : bond 0.03325 ( 340) hydrogen bonds : angle 4.35473 ( 993) link_BETA1-4 : bond 0.00525 ( 1) link_BETA1-4 : angle 0.77493 ( 3) link_NAG-ASN : bond 0.00541 ( 1) link_NAG-ASN : angle 4.57744 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.221 Fit side-chains REVERT: A 188 TRP cc_start: 0.7379 (m100) cc_final: 0.7049 (m100) REVERT: A 297 MET cc_start: 0.7825 (tmm) cc_final: 0.5342 (mtt) REVERT: A 447 TYR cc_start: 0.7529 (OUTLIER) cc_final: 0.6553 (m-80) REVERT: A 471 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8179 (mp) REVERT: B 23 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8113 (mp) outliers start: 33 outliers final: 28 residues processed: 97 average time/residue: 0.0485 time to fit residues: 7.1767 Evaluate side-chains 96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 61 GLN Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.0970 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.0270 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 overall best weight: 0.3236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.185044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.161721 restraints weight = 6700.793| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.54 r_work: 0.3771 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6391 Z= 0.112 Angle : 0.516 7.660 8717 Z= 0.261 Chirality : 0.040 0.347 972 Planarity : 0.003 0.029 1053 Dihedral : 6.802 52.473 1105 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 5.28 % Allowed : 27.48 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.76 (0.32), residues: 759 helix: 1.43 (0.26), residues: 375 sheet: 0.63 (0.54), residues: 114 loop : -0.82 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 69 TYR 0.017 0.001 TYR A 387 PHE 0.024 0.001 PHE A 477 TRP 0.018 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 6386) covalent geometry : angle 0.50964 ( 8705) SS BOND : bond 0.00290 ( 3) SS BOND : angle 1.10366 ( 6) hydrogen bonds : bond 0.03266 ( 340) hydrogen bonds : angle 4.35471 ( 993) link_BETA1-4 : bond 0.00314 ( 1) link_BETA1-4 : angle 0.83796 ( 3) link_NAG-ASN : bond 0.00585 ( 1) link_NAG-ASN : angle 4.26470 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.225 Fit side-chains REVERT: A 188 TRP cc_start: 0.7358 (m100) cc_final: 0.7044 (m100) REVERT: A 297 MET cc_start: 0.7828 (tmm) cc_final: 0.5409 (mtt) REVERT: A 407 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6515 (tmm) REVERT: A 420 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6664 (mp) REVERT: A 447 TYR cc_start: 0.7535 (OUTLIER) cc_final: 0.6555 (m-80) REVERT: A 471 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 23 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8133 (mp) outliers start: 34 outliers final: 25 residues processed: 96 average time/residue: 0.0538 time to fit residues: 7.7438 Evaluate side-chains 96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 0.0870 chunk 55 optimal weight: 0.6980 chunk 52 optimal weight: 10.0000 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.182257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.156929 restraints weight = 6627.340| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.07 r_work: 0.3737 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6391 Z= 0.131 Angle : 0.527 7.855 8717 Z= 0.267 Chirality : 0.040 0.355 972 Planarity : 0.003 0.029 1053 Dihedral : 6.721 52.099 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.12 % Allowed : 27.64 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.68 (0.32), residues: 759 helix: 1.36 (0.26), residues: 375 sheet: 0.59 (0.53), residues: 114 loop : -0.86 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 69 TYR 0.017 0.001 TYR A 387 PHE 0.026 0.001 PHE A 477 TRP 0.018 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 6386) covalent geometry : angle 0.51978 ( 8705) SS BOND : bond 0.00333 ( 3) SS BOND : angle 1.24859 ( 6) hydrogen bonds : bond 0.03366 ( 340) hydrogen bonds : angle 4.38438 ( 993) link_BETA1-4 : bond 0.00387 ( 1) link_BETA1-4 : angle 0.82425 ( 3) link_NAG-ASN : bond 0.00450 ( 1) link_NAG-ASN : angle 4.37578 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1518 Ramachandran restraints generated. 759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.233 Fit side-chains REVERT: A 188 TRP cc_start: 0.7299 (m100) cc_final: 0.6978 (m100) REVERT: A 297 MET cc_start: 0.7741 (tmm) cc_final: 0.5326 (mtt) REVERT: A 407 MET cc_start: 0.6651 (OUTLIER) cc_final: 0.6390 (tmm) REVERT: A 420 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6548 (mp) REVERT: A 447 TYR cc_start: 0.7517 (OUTLIER) cc_final: 0.6514 (m-80) REVERT: A 471 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8189 (mp) REVERT: A 605 TYR cc_start: 0.7062 (t80) cc_final: 0.6716 (t80) REVERT: B 23 LEU cc_start: 0.8281 (OUTLIER) cc_final: 0.7976 (mp) outliers start: 33 outliers final: 26 residues processed: 98 average time/residue: 0.0513 time to fit residues: 7.7363 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 447 TYR Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 577 CYS Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 62 GLN Chi-restraints excluded: chain C residue 99 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 28 optimal weight: 0.0770 chunk 24 optimal weight: 0.3980 chunk 72 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.186021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.159253 restraints weight = 6593.936| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.33 r_work: 0.3754 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6391 Z= 0.104 Angle : 0.510 7.808 8717 Z= 0.259 Chirality : 0.039 0.332 972 Planarity : 0.003 0.028 1053 Dihedral : 6.511 52.633 1105 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.50 % Allowed : 28.26 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % 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: 0.80 (0.32), residues: 759 helix: 1.47 (0.26), residues: 374 sheet: 0.66 (0.53), residues: 114 loop : -0.82 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 117 TYR 0.016 0.001 TYR A 387 PHE 0.021 0.001 PHE A 477 TRP 0.021 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 6386) covalent geometry : angle 0.50380 ( 8705) SS BOND : bond 0.00256 ( 3) SS BOND : angle 1.01148 ( 6) hydrogen bonds : bond 0.03197 ( 340) hydrogen bonds : angle 4.31793 ( 993) link_BETA1-4 : bond 0.00436 ( 1) link_BETA1-4 : angle 0.92972 ( 3) link_NAG-ASN : bond 0.00669 ( 1) link_NAG-ASN : angle 3.98042 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1684.10 seconds wall clock time: 29 minutes 34.24 seconds (1774.24 seconds total)