Starting phenix.real_space_refine on Thu Jul 2 04:49:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8de3_27383/07_2026/8de3_27383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de3_27383/07_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_27383/07_2026/8de3_27383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de3_27383/07_2026/8de3_27383.map" model { file = "/net/cci-nas-00/data/ceres_data/8de3_27383/07_2026/8de3_27383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de3_27383/07_2026/8de3_27383.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8de3_27383/07_2026/8de3_27383.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8de3_27383/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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 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: 1.42, per 1000 atoms: 0.23 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: 0.57 Conformation dependent library (CDL) restraints added in 522.2 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: 0.12 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: 0.67 Time building geometry restraints manager: 0.68 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: 3031 17.36 - 34.73: 408 34.73 - 52.09: 120 52.09 - 69.45: 17 69.45 - 86.82: 6 Dihedral angle restraints: 3582 sinusoidal: 1384 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 3579 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: 5.060 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.870 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 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 : 16.928 86.818 2177 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/Z covalent geometry : bond 0.00848 / 0.42 ( 6386) covalent geometry : angle 0.68725 / 0.28 ( 8705) SS BOND : bond 0.00078 / 0.04 ( 3) SS BOND : angle 0.17621 / 0.10 ( 6) hydrogen bonds : bond 0.17141 / 11.26 ( 340) hydrogen bonds : angle 5.95978 / 4.47 ( 993) link_BETA1-4 : bond 0.00290 / 0.15 ( 1) link_BETA1-4 : angle 0.86513 / 0.46 ( 3) link_NAG-ASN : bond 0.00711 / 0.37 ( 1) link_NAG-ASN : angle 1.72909 / 0.91 ( 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 : 0.144 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: 0.0531 time to fit residues: 5.5870 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 : 0.195 ------------------------------------------------------------------------------- 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... ** 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 = 0.4348 r_free = 0.4348 target = 0.197826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.174925 restraints weight = 6627.891| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.84 r_work: 0.3938 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.0970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6391 Z= 0.115 Angle : 0.501 6.467 8717 Z= 0.253 Chirality : 0.038 0.188 972 Planarity : 0.004 0.056 1053 Dihedral : 6.481 55.542 868 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.71 % Allowed : 28.42 % 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: 1.14 (0.32), residues: 759 helix: 1.89 (0.26), residues: 371 sheet: 0.61 (0.55), residues: 114 loop : -0.76 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 644 TYR 0.012 0.001 TYR A 212 PHE 0.020 0.001 PHE A 477 TRP 0.008 0.001 TRP B 66 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 6386) covalent geometry : angle 0.49901 / 0.25 ( 8705) SS BOND : bond 0.00356 / 0.18 ( 3) SS BOND : angle 0.89923 / 0.45 ( 6) hydrogen bonds : bond 0.03261 / 2.12 ( 340) hydrogen bonds : angle 4.45985 / 3.30 ( 993) link_BETA1-4 : bond 0.00576 / 0.30 ( 1) link_BETA1-4 : angle 0.94078 / 0.53 ( 3) link_NAG-ASN : bond 0.00363 / 0.19 ( 1) link_NAG-ASN : angle 1.81580 / 0.94 ( 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 85 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.122 Fit side-chains REVERT: A 297 MET cc_start: 0.7681 (tmm) cc_final: 0.5345 (mtt) REVERT: A 471 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7984 (mp) outliers start: 11 outliers final: 5 residues processed: 85 average time/residue: 0.0460 time to fit residues: 5.7622 Evaluate side-chains 80 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.208 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 61 optimal weight: 0.0050 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 0.0370 chunk 27 optimal weight: 1.9990 overall best weight: 0.3730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4312 r_free = 0.4312 target = 0.192263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.172644 restraints weight = 6427.081| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 1.22 r_work: 0.3930 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3799 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1566 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= 0.116 Angle : 0.489 5.918 8717 Z= 0.247 Chirality : 0.040 0.353 972 Planarity : 0.003 0.044 1053 Dihedral : 5.964 55.009 867 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.80 % Allowed : 28.57 % Favored : 68.63 % 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: 0.94 (0.32), residues: 759 helix: 1.68 (0.26), residues: 371 sheet: 0.66 (0.54), residues: 114 loop : -0.85 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 427 TYR 0.013 0.001 TYR A 212 PHE 0.024 0.001 PHE A 477 TRP 0.008 0.001 TRP B 66 HIS 0.001 0.000 HIS A 260 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 6386) covalent geometry : angle 0.48401 / 0.25 ( 8705) SS BOND : bond 0.00298 / 0.15 ( 3) SS BOND : angle 0.90102 / 0.49 ( 6) hydrogen bonds : bond 0.03299 / 2.16 ( 340) hydrogen bonds : angle 4.28116 / 3.19 ( 993) link_BETA1-4 : bond 0.00502 / 0.26 ( 1) link_BETA1-4 : angle 1.02069 / 0.55 ( 3) link_NAG-ASN : bond 0.01254 / 0.66 ( 1) link_NAG-ASN : angle 3.65743 / 1.87 ( 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 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.164 Fit side-chains REVERT: A 297 MET cc_start: 0.7777 (tmm) cc_final: 0.5421 (mtt) REVERT: A 471 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8031 (mp) outliers start: 18 outliers final: 8 residues processed: 89 average time/residue: 0.0540 time to fit residues: 7.0572 Evaluate side-chains 80 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU 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 B residue 56 VAL Chi-restraints excluded: chain B residue 90 THR 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: 0.6980 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 17 optimal weight: 0.0770 chunk 0 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 27 optimal weight: 0.1980 chunk 9 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4265 r_free = 0.4265 target = 0.189257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.170576 restraints weight = 6601.964| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 1.08 r_work: 0.3871 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1839 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= 0.115 Angle : 0.495 6.545 8717 Z= 0.251 Chirality : 0.039 0.266 972 Planarity : 0.003 0.039 1053 Dihedral : 5.999 58.165 867 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.95 % Allowed : 28.57 % Favored : 68.48 % 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: 0.89 (0.32), residues: 759 helix: 1.60 (0.26), residues: 374 sheet: 0.66 (0.53), residues: 114 loop : -0.85 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 38 TYR 0.015 0.001 TYR A 605 PHE 0.021 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/Z covalent geometry : bond 0.00258 / 0.11 ( 6386) covalent geometry : angle 0.48935 / 0.25 ( 8705) SS BOND : bond 0.00546 / 0.27 ( 3) SS BOND : angle 0.92981 / 0.48 ( 6) hydrogen bonds : bond 0.03153 / 2.08 ( 340) hydrogen bonds : angle 4.27059 / 3.18 ( 993) link_BETA1-4 : bond 0.00252 / 0.13 ( 1) link_BETA1-4 : angle 0.80254 / 0.45 ( 3) link_NAG-ASN : bond 0.00427 / 0.22 ( 1) link_NAG-ASN : angle 3.70408 / 1.91 ( 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 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.219 Fit side-chains REVERT: A 297 MET cc_start: 0.7872 (tmm) cc_final: 0.5512 (mtt) REVERT: A 471 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8116 (mp) outliers start: 19 outliers final: 14 residues processed: 85 average time/residue: 0.0551 time to fit residues: 6.9359 Evaluate side-chains 84 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 418 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 602 LEU Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain C residue 24 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 0.0030 chunk 3 optimal weight: 0.0040 chunk 43 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 overall best weight: 0.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4292 r_free = 0.4292 target = 0.191722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.167931 restraints weight = 6668.900| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 1.52 r_work: 0.3836 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2092 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= 0.119 Angle : 0.494 5.790 8717 Z= 0.252 Chirality : 0.039 0.261 972 Planarity : 0.003 0.035 1053 Dihedral : 5.879 52.859 867 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.66 % Allowed : 27.33 % 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: 0.85 (0.32), residues: 759 helix: 1.56 (0.26), residues: 375 sheet: 0.66 (0.53), residues: 114 loop : -0.89 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 38 TYR 0.015 0.001 TYR A 387 PHE 0.020 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/Z covalent geometry : bond 0.00272 / 0.12 ( 6386) covalent geometry : angle 0.48948 / 0.25 ( 8705) SS BOND : bond 0.00283 / 0.14 ( 3) SS BOND : angle 1.22261 / 0.59 ( 6) hydrogen bonds : bond 0.03213 / 2.13 ( 340) hydrogen bonds : angle 4.26923 / 3.17 ( 993) link_BETA1-4 : bond 0.00281 / 0.15 ( 1) link_BETA1-4 : angle 0.76427 / 0.43 ( 3) link_NAG-ASN : bond 0.00355 / 0.19 ( 1) link_NAG-ASN : angle 3.29843 / 1.69 ( 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 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.209 Fit side-chains REVERT: A 223 TYR cc_start: 0.8707 (OUTLIER) cc_final: 0.8006 (m-80) REVERT: A 297 MET cc_start: 0.7750 (tmm) cc_final: 0.5343 (mtt) REVERT: A 471 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8034 (mp) REVERT: A 595 MET cc_start: 0.7136 (ttm) cc_final: 0.6742 (ttp) outliers start: 30 outliers final: 20 residues processed: 93 average time/residue: 0.0515 time to fit residues: 7.2091 Evaluate side-chains 88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 223 TYR Chi-restraints excluded: chain A residue 256 THR 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 59 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 37 optimal weight: 0.0010 chunk 67 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 66 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 46 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4224 r_free = 0.4224 target = 0.185390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.159243 restraints weight = 6655.616| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.16 r_work: 0.3751 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2403 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= 0.132 Angle : 0.521 6.970 8717 Z= 0.264 Chirality : 0.040 0.271 972 Planarity : 0.003 0.032 1053 Dihedral : 5.900 55.962 867 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.81 % Allowed : 27.02 % Favored : 68.17 % 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: 0.78 (0.32), residues: 759 helix: 1.50 (0.26), residues: 374 sheet: 0.63 (0.53), residues: 114 loop : -0.90 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 38 TYR 0.018 0.002 TYR A 387 PHE 0.019 0.001 PHE A 477 TRP 0.014 0.001 TRP A 234 HIS 0.001 0.000 HIS A 180 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 6386) covalent geometry : angle 0.51526 / 0.26 ( 8705) SS BOND : bond 0.00348 / 0.18 ( 3) SS BOND : angle 1.28906 / 0.63 ( 6) hydrogen bonds : bond 0.03355 / 2.24 ( 340) hydrogen bonds : angle 4.33663 / 3.22 ( 993) link_BETA1-4 : bond 0.00352 / 0.19 ( 1) link_BETA1-4 : angle 0.78892 / 0.44 ( 3) link_NAG-ASN : bond 0.00220 / 0.12 ( 1) link_NAG-ASN : angle 3.73443 / 1.93 ( 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 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 69 time to evaluate : 0.202 Fit side-chains REVERT: A 188 TRP cc_start: 0.7308 (m100) cc_final: 0.6977 (m100) REVERT: A 297 MET cc_start: 0.7751 (tmm) cc_final: 0.5270 (mtt) REVERT: A 420 LEU cc_start: 0.7076 (OUTLIER) cc_final: 0.6407 (mp) REVERT: A 471 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8073 (mp) outliers start: 31 outliers final: 22 residues processed: 94 average time/residue: 0.0493 time to fit residues: 7.1029 Evaluate side-chains 90 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.206 ------------------------------------------------------------------------------- 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 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 594 LEU 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 B residue 103 SER Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 32 optimal weight: 0.2980 chunk 56 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 0.0670 chunk 72 optimal weight: 0.9980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.186535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161093 restraints weight = 6681.511| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.07 r_work: 0.3753 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2426 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= 0.116 Angle : 0.514 6.981 8717 Z= 0.259 Chirality : 0.040 0.370 972 Planarity : 0.003 0.029 1053 Dihedral : 5.980 58.453 867 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.18 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: 0.84 (0.32), residues: 759 helix: 1.51 (0.26), residues: 375 sheet: 0.67 (0.53), residues: 114 loop : -0.83 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 38 TYR 0.018 0.001 TYR A 387 PHE 0.015 0.001 PHE A 477 TRP 0.013 0.001 TRP A 234 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 ( 6386) covalent geometry : angle 0.50601 / 0.26 ( 8705) SS BOND : bond 0.00335 / 0.17 ( 3) SS BOND : angle 1.15572 / 0.59 ( 6) hydrogen bonds : bond 0.03246 / 2.16 ( 340) hydrogen bonds : angle 4.29313 / 3.16 ( 993) link_BETA1-4 : bond 0.00716 / 0.38 ( 1) link_BETA1-4 : angle 0.88061 / 0.51 ( 3) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 4.62870 / 2.38 ( 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 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 0.218 Fit side-chains REVERT: A 297 MET cc_start: 0.7763 (tmm) cc_final: 0.5324 (mtt) REVERT: A 420 LEU cc_start: 0.7046 (OUTLIER) cc_final: 0.6423 (mp) REVERT: A 447 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6509 (m-80) REVERT: A 471 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8167 (mp) outliers start: 33 outliers final: 24 residues processed: 95 average time/residue: 0.0528 time to fit residues: 7.6046 Evaluate side-chains 94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 67 time to evaluate : 0.197 ------------------------------------------------------------------------------- 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 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 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 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 33 VAL 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: 0.8980 chunk 36 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 39 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4187 r_free = 0.4187 target = 0.181728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.161099 restraints weight = 6764.624| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.23 r_work: 0.3756 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6391 Z= 0.151 Angle : 0.543 6.525 8717 Z= 0.276 Chirality : 0.041 0.330 972 Planarity : 0.004 0.028 1053 Dihedral : 5.974 54.070 867 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 4.97 % Allowed : 27.02 % 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: 0.66 (0.32), residues: 759 helix: 1.34 (0.26), residues: 373 sheet: 0.64 (0.54), residues: 114 loop : -0.89 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 69 TYR 0.018 0.002 TYR A 387 PHE 0.027 0.001 PHE A 477 TRP 0.013 0.001 TRP A 234 HIS 0.000 0.000 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 ( 6386) covalent geometry : angle 0.53380 / 0.27 ( 8705) SS BOND : bond 0.00439 / 0.22 ( 3) SS BOND : angle 1.41315 / 0.70 ( 6) hydrogen bonds : bond 0.03586 / 2.39 ( 340) hydrogen bonds : angle 4.42651 / 3.26 ( 993) link_BETA1-4 : bond 0.00351 / 0.18 ( 1) link_BETA1-4 : angle 0.73328 / 0.40 ( 3) link_NAG-ASN : bond 0.00405 / 0.21 ( 1) link_NAG-ASN : angle 4.94154 / 2.55 ( 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 99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.218 Fit side-chains REVERT: A 188 TRP cc_start: 0.7436 (m100) cc_final: 0.7128 (m100) REVERT: A 297 MET cc_start: 0.7893 (tmm) cc_final: 0.5461 (mtt) REVERT: A 407 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6581 (tmm) REVERT: A 420 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6649 (mp) REVERT: A 447 TYR cc_start: 0.7519 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: A 471 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8164 (mp) outliers start: 32 outliers final: 24 residues processed: 94 average time/residue: 0.0511 time to fit residues: 7.3205 Evaluate side-chains 94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 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 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 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 B residue 103 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.0370 chunk 29 optimal weight: 0.8980 chunk 3 optimal weight: 0.0870 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 55 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4189 r_free = 0.4189 target = 0.182097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.158678 restraints weight = 6710.810| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.57 r_work: 0.3734 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2719 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= 0.127 Angle : 0.526 7.013 8717 Z= 0.265 Chirality : 0.040 0.371 972 Planarity : 0.003 0.028 1053 Dihedral : 5.673 54.585 867 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.66 % Allowed : 27.64 % 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: 0.68 (0.32), residues: 759 helix: 1.35 (0.26), residues: 375 sheet: 0.62 (0.53), residues: 114 loop : -0.87 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 38 TYR 0.017 0.001 TYR A 387 PHE 0.027 0.001 PHE A 348 TRP 0.015 0.001 TRP A 234 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 6386) covalent geometry : angle 0.51738 / 0.26 ( 8705) SS BOND : bond 0.00330 / 0.16 ( 3) SS BOND : angle 1.15215 / 0.56 ( 6) hydrogen bonds : bond 0.03393 / 2.26 ( 340) hydrogen bonds : angle 4.36925 / 3.20 ( 993) link_BETA1-4 : bond 0.00370 / 0.19 ( 1) link_BETA1-4 : angle 0.77376 / 0.44 ( 3) link_NAG-ASN : bond 0.00749 / 0.39 ( 1) link_NAG-ASN : angle 4.80172 / 2.46 ( 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 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 68 time to evaluate : 0.203 Fit side-chains REVERT: A 188 TRP cc_start: 0.7319 (m100) cc_final: 0.7028 (m100) REVERT: A 297 MET cc_start: 0.7796 (tmm) cc_final: 0.5354 (mtt) REVERT: A 407 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6469 (tmm) REVERT: A 420 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6474 (mp) REVERT: A 447 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.6515 (m-80) REVERT: A 471 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8175 (mp) outliers start: 30 outliers final: 24 residues processed: 93 average time/residue: 0.0555 time to fit residues: 7.6736 Evaluate side-chains 94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.196 ------------------------------------------------------------------------------- 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 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 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 617 CYS Chi-restraints excluded: chain B residue 37 VAL 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 B residue 103 SER Chi-restraints excluded: chain B residue 127 MET 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: 0.3980 chunk 23 optimal weight: 0.0980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4214 r_free = 0.4214 target = 0.184788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.161212 restraints weight = 6615.846| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 1.51 r_work: 0.3770 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2710 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= 0.117 Angle : 0.516 6.619 8717 Z= 0.263 Chirality : 0.040 0.336 972 Planarity : 0.003 0.027 1053 Dihedral : 5.473 53.799 867 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.04 % Allowed : 28.11 % 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: 0.74 (0.32), residues: 759 helix: 1.41 (0.26), residues: 375 sheet: 0.62 (0.53), residues: 114 loop : -0.84 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 644 TYR 0.019 0.001 TYR A 387 PHE 0.025 0.001 PHE A 477 TRP 0.025 0.001 TRP A 234 HIS 0.001 0.000 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6386) covalent geometry : angle 0.50918 / 0.26 ( 8705) SS BOND : bond 0.00322 / 0.16 ( 3) SS BOND : angle 1.11640 / 0.55 ( 6) hydrogen bonds : bond 0.03301 / 2.19 ( 340) hydrogen bonds : angle 4.32344 / 3.17 ( 993) link_BETA1-4 : bond 0.00402 / 0.21 ( 1) link_BETA1-4 : angle 0.78701 / 0.43 ( 3) link_NAG-ASN : bond 0.00635 / 0.33 ( 1) link_NAG-ASN : angle 4.37688 / 2.24 ( 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 93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.167 Fit side-chains REVERT: A 188 TRP cc_start: 0.7391 (m100) cc_final: 0.7103 (m100) REVERT: A 297 MET cc_start: 0.7830 (tmm) cc_final: 0.5427 (mtt) REVERT: A 407 MET cc_start: 0.6781 (OUTLIER) cc_final: 0.6524 (tmm) REVERT: A 420 LEU cc_start: 0.7188 (OUTLIER) cc_final: 0.6596 (mp) REVERT: A 447 TYR cc_start: 0.7518 (OUTLIER) cc_final: 0.6581 (m-80) REVERT: A 471 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8173 (mp) outliers start: 26 outliers final: 22 residues processed: 89 average time/residue: 0.0516 time to fit residues: 6.8901 Evaluate side-chains 92 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 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 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 617 CYS Chi-restraints excluded: chain B residue 37 VAL 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=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: 0.3980 chunk 9 optimal weight: 0.0980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 28 optimal weight: 2.9990 chunk 24 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4205 r_free = 0.4205 target = 0.183871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.161085 restraints weight = 6568.084| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.79 r_work: 0.3767 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2712 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= 0.117 Angle : 0.524 8.766 8717 Z= 0.264 Chirality : 0.040 0.332 972 Planarity : 0.003 0.028 1053 Dihedral : 5.392 53.436 867 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.66 % Allowed : 27.80 % Favored : 67.55 % 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 (0.31), residues: 759 helix: 1.41 (0.26), residues: 375 sheet: 0.66 (0.53), residues: 114 loop : -0.86 (0.41), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 644 TYR 0.018 0.001 TYR A 387 PHE 0.042 0.001 PHE A 477 TRP 0.019 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 6386) covalent geometry : angle 0.51761 / 0.26 ( 8705) SS BOND : bond 0.00321 / 0.16 ( 3) SS BOND : angle 1.06399 / 0.52 ( 6) hydrogen bonds : bond 0.03273 / 2.18 ( 340) hydrogen bonds : angle 4.31658 / 3.16 ( 993) link_BETA1-4 : bond 0.00369 / 0.19 ( 1) link_BETA1-4 : angle 0.84239 / 0.46 ( 3) link_NAG-ASN : bond 0.00530 / 0.28 ( 1) link_NAG-ASN : angle 4.09459 / 2.09 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1629.36 seconds wall clock time: 28 minutes 48.95 seconds (1728.95 seconds total)