Starting phenix.real_space_refine on Tue Feb 11 22:46:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de3_27383/02_2025/8de3_27383.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de3_27383/02_2025/8de3_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_27383/02_2025/8de3_27383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de3_27383/02_2025/8de3_27383.map" model { file = "/net/cci-nas-00/data/ceres_data/8de3_27383/02_2025/8de3_27383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de3_27383/02_2025/8de3_27383.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.020 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.05, per 1000 atoms: 0.81 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: 1.80 Conformation dependent library (CDL) restraints added in 820.3 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: 0.68 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: 1.54 Time building geometry restraints manager: 2.05 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: 3.120 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.680 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.120 ------------------------------------------------------------------------------- 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 6386 Z= 0.550 Angle : 0.687 12.253 8705 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.009 0.001 TRP A 234 HIS 0.001 0.000 HIS A 493 PHE 0.021 0.001 PHE A 348 TYR 0.008 0.001 TYR A 212 ARG 0.001 0.000 ARG C 38 *********************** 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 : 0.616 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: 0.1507 time to fit residues: 15.4945 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 : 0.611 ------------------------------------------------------------------------------- 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 63 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4279 r_free = 0.4279 target = 0.188828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.167488 restraints weight = 6386.972| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.74 r_work: 0.3863 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6386 Z= 0.256 Angle : 0.575 6.005 8705 Z= 0.291 Chirality : 0.042 0.270 972 Planarity : 0.004 0.057 1053 Dihedral : 8.554 59.653 1106 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.33 % Allowed : 28.73 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.32), residues: 759 helix: 1.52 (0.26), residues: 370 sheet: 0.58 (0.56), residues: 114 loop : -0.92 (0.41), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 55 HIS 0.001 0.001 HIS A 260 PHE 0.028 0.002 PHE A 477 TYR 0.018 0.002 TYR A 212 ARG 0.003 0.000 ARG B 47 *********************** 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 88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.631 Fit side-chains REVERT: A 217 MET cc_start: 0.8055 (mmm) cc_final: 0.7811 (mmm) REVERT: A 297 MET cc_start: 0.7917 (tmm) cc_final: 0.5518 (mtt) REVERT: A 471 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8069 (mp) outliers start: 15 outliers final: 7 residues processed: 86 average time/residue: 0.1411 time to fit residues: 17.7592 Evaluate side-chains 77 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 172 MET 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 56 VAL 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 6 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 45 optimal weight: 0.0970 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.191944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.168452 restraints weight = 6604.688| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.53 r_work: 0.3835 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6386 Z= 0.182 Angle : 0.502 6.219 8705 Z= 0.254 Chirality : 0.041 0.377 972 Planarity : 0.004 0.046 1053 Dihedral : 7.563 59.329 1105 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.11 % Allowed : 28.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.32), residues: 759 helix: 1.56 (0.26), residues: 371 sheet: 0.58 (0.55), residues: 114 loop : -0.93 (0.42), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.001 0.000 HIS C 100 PHE 0.016 0.001 PHE A 477 TYR 0.012 0.001 TYR A 387 ARG 0.002 0.000 ARG C 38 *********************** 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 86 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 66 time to evaluate : 0.568 Fit side-chains REVERT: A 297 MET cc_start: 0.7829 (tmm) cc_final: 0.5388 (mtt) REVERT: A 471 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7991 (mp) outliers start: 20 outliers final: 11 residues processed: 80 average time/residue: 0.1409 time to fit residues: 16.4161 Evaluate side-chains 76 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.691 ------------------------------------------------------------------------------- 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 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 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 1 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4183 r_free = 0.4183 target = 0.181343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.157542 restraints weight = 6794.897| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 1.56 r_work: 0.3721 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3578 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6386 Z= 0.271 Angle : 0.559 5.502 8705 Z= 0.288 Chirality : 0.042 0.333 972 Planarity : 0.004 0.040 1053 Dihedral : 7.584 59.311 1105 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.32), residues: 759 helix: 1.20 (0.26), residues: 373 sheet: 0.53 (0.54), residues: 114 loop : -1.04 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 574 HIS 0.001 0.000 HIS C 100 PHE 0.026 0.002 PHE A 477 TYR 0.016 0.002 TYR A 212 ARG 0.002 0.000 ARG B 69 *********************** 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 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.653 Fit side-chains REVERT: A 297 MET cc_start: 0.7958 (tmm) cc_final: 0.5489 (mtt) REVERT: A 420 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.6749 (mp) REVERT: A 471 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8137 (mp) outliers start: 33 outliers final: 23 residues processed: 96 average time/residue: 0.1373 time to fit residues: 19.3485 Evaluate side-chains 87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 62 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 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 62 LYS 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 99 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 58 optimal weight: 0.8980 chunk 60 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.4227 r_free = 0.4227 target = 0.185023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.161065 restraints weight = 6598.067| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 1.51 r_work: 0.3764 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 6386 Z= 0.223 Angle : 0.528 6.783 8705 Z= 0.270 Chirality : 0.041 0.372 972 Planarity : 0.004 0.036 1053 Dihedral : 7.581 58.488 1105 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.28 % Allowed : 27.64 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.32), residues: 759 helix: 1.25 (0.26), residues: 373 sheet: 0.53 (0.55), residues: 114 loop : -1.02 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.014 0.001 PHE A 603 TYR 0.016 0.001 TYR A 387 ARG 0.002 0.000 ARG A 116 *********************** 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 101 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 67 time to evaluate : 0.672 Fit side-chains REVERT: A 297 MET cc_start: 0.7931 (tmm) cc_final: 0.5457 (mtt) REVERT: A 420 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6674 (mp) REVERT: A 447 TYR cc_start: 0.7652 (OUTLIER) cc_final: 0.6600 (m-80) REVERT: A 471 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8195 (mp) outliers start: 34 outliers final: 26 residues processed: 97 average time/residue: 0.1391 time to fit residues: 19.6438 Evaluate side-chains 94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 256 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 330 SER 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 539 LEU 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 40 SER Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 57 optimal weight: 0.8980 chunk 40 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 64 optimal weight: 0.0070 chunk 73 optimal weight: 0.9980 chunk 2 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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** A 392 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.185397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 101)---------------| | r_work = 0.3933 r_free = 0.3933 target = 0.159184 restraints weight = 6619.665| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 2.28 r_work: 0.3757 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6386 Z= 0.148 Angle : 0.490 5.924 8705 Z= 0.252 Chirality : 0.040 0.358 972 Planarity : 0.003 0.033 1053 Dihedral : 7.305 57.648 1105 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.81 % Allowed : 27.80 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.32), residues: 759 helix: 1.48 (0.26), residues: 373 sheet: 0.54 (0.54), residues: 114 loop : -0.88 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.001 0.000 HIS A 260 PHE 0.014 0.001 PHE A 603 TYR 0.016 0.001 TYR A 387 ARG 0.001 0.000 ARG B 69 *********************** 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 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.649 Fit side-chains REVERT: A 297 MET cc_start: 0.7772 (tmm) cc_final: 0.5270 (mtt) REVERT: A 420 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6422 (mp) REVERT: A 447 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.6468 (m-80) REVERT: A 471 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8097 (mp) REVERT: A 477 PHE cc_start: 0.7700 (m-10) cc_final: 0.7153 (m-10) outliers start: 31 outliers final: 19 residues processed: 95 average time/residue: 0.1326 time to fit residues: 18.5615 Evaluate side-chains 86 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 64 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 330 SER Chi-restraints excluded: chain A residue 392 ASN 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 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 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 49 optimal weight: 0.0050 chunk 38 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.4203 r_free = 0.4203 target = 0.183378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.156992 restraints weight = 6681.540| |-----------------------------------------------------------------------------| r_work (start): 0.3914 rms_B_bonded: 2.06 r_work: 0.3719 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6386 Z= 0.198 Angle : 0.517 6.504 8705 Z= 0.263 Chirality : 0.041 0.372 972 Planarity : 0.003 0.031 1053 Dihedral : 7.323 57.309 1105 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 5.75 % Allowed : 27.64 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.32), residues: 759 helix: 1.43 (0.26), residues: 372 sheet: 0.53 (0.54), residues: 114 loop : -0.92 (0.41), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.017 0.001 PHE A 603 TYR 0.015 0.001 TYR A 387 ARG 0.001 0.000 ARG B 69 *********************** 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 100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.615 Fit side-chains REVERT: A 188 TRP cc_start: 0.7321 (m100) cc_final: 0.7008 (m100) REVERT: A 297 MET cc_start: 0.7775 (tmm) cc_final: 0.5278 (mtt) REVERT: A 420 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6464 (mp) REVERT: A 447 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6500 (m-80) REVERT: A 471 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8111 (mp) outliers start: 37 outliers final: 26 residues processed: 95 average time/residue: 0.1507 time to fit residues: 20.9477 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 : 0.638 ------------------------------------------------------------------------------- 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 330 SER 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 539 LEU 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 51 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 62 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 53 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.178354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.153844 restraints weight = 6667.755| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.10 r_work: 0.3662 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6386 Z= 0.286 Angle : 0.586 6.855 8705 Z= 0.299 Chirality : 0.043 0.384 972 Planarity : 0.004 0.029 1053 Dihedral : 7.495 58.079 1105 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 6.21 % Allowed : 27.80 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.32), residues: 759 helix: 1.08 (0.26), residues: 372 sheet: 0.45 (0.55), residues: 114 loop : -1.03 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 234 HIS 0.001 0.000 HIS A 180 PHE 0.020 0.002 PHE A 603 TYR 0.018 0.002 TYR A 387 ARG 0.002 0.000 ARG B 69 *********************** 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 107 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 67 time to evaluate : 0.608 Fit side-chains REVERT: A 188 TRP cc_start: 0.7444 (m100) cc_final: 0.7120 (m100) REVERT: A 228 PHE cc_start: 0.7708 (m-80) cc_final: 0.7434 (m-80) REVERT: A 297 MET cc_start: 0.7851 (tmm) cc_final: 0.5367 (mtt) REVERT: A 420 LEU cc_start: 0.7061 (OUTLIER) cc_final: 0.6553 (mp) REVERT: A 447 TYR cc_start: 0.7593 (OUTLIER) cc_final: 0.6574 (m-80) REVERT: A 471 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8086 (mp) outliers start: 40 outliers final: 31 residues processed: 103 average time/residue: 0.1292 time to fit residues: 19.5730 Evaluate side-chains 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 64 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 302 ILE Chi-restraints excluded: chain A residue 330 SER 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 483 VAL Chi-restraints excluded: chain A residue 495 TRP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 539 LEU 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 A residue 630 ILE Chi-restraints excluded: chain A residue 631 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 0.4980 chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 ** 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 = 0.4170 r_free = 0.4170 target = 0.179437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.156326 restraints weight = 6651.431| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.59 r_work: 0.3724 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6386 Z= 0.210 Angle : 0.544 7.547 8705 Z= 0.277 Chirality : 0.042 0.387 972 Planarity : 0.004 0.030 1053 Dihedral : 7.294 58.242 1105 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.97 % Allowed : 29.04 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.31), residues: 759 helix: 1.17 (0.26), residues: 373 sheet: 0.44 (0.54), residues: 114 loop : -0.96 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.021 0.001 PHE A 348 TYR 0.020 0.001 TYR A 387 ARG 0.001 0.000 ARG A 344 *********************** 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 96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 64 time to evaluate : 0.608 Fit side-chains revert: symmetry clash REVERT: A 188 TRP cc_start: 0.7426 (m100) cc_final: 0.7118 (m100) REVERT: A 228 PHE cc_start: 0.7752 (m-80) cc_final: 0.7452 (m-80) REVERT: A 297 MET cc_start: 0.7919 (tmm) cc_final: 0.5487 (mtt) REVERT: A 420 LEU cc_start: 0.7185 (OUTLIER) cc_final: 0.6639 (mp) REVERT: A 447 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.6668 (m-80) REVERT: A 471 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8123 (mp) outliers start: 32 outliers final: 28 residues processed: 94 average time/residue: 0.1285 time to fit residues: 17.7145 Evaluate side-chains 94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.599 ------------------------------------------------------------------------------- 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 330 SER Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 419 VAL 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 539 LEU 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 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 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 40 optimal weight: 0.0980 chunk 45 optimal weight: 0.0770 chunk 68 optimal weight: 0.3980 chunk 36 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.4192 r_free = 0.4192 target = 0.181733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.155341 restraints weight = 6619.069| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.61 r_work: 0.3748 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6386 Z= 0.163 Angle : 0.509 6.255 8705 Z= 0.261 Chirality : 0.040 0.345 972 Planarity : 0.003 0.030 1053 Dihedral : 7.057 56.393 1105 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.81 % Allowed : 29.04 % Favored : 66.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.31), residues: 759 helix: 1.32 (0.26), residues: 374 sheet: 0.52 (0.53), residues: 114 loop : -0.89 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 234 HIS 0.001 0.000 HIS A 180 PHE 0.016 0.001 PHE A 603 TYR 0.018 0.001 TYR A 387 ARG 0.001 0.000 ARG B 69 ********************** 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 98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.631 Fit side-chains REVERT: A 188 TRP cc_start: 0.7361 (m100) cc_final: 0.7057 (m100) REVERT: A 228 PHE cc_start: 0.7736 (m-80) cc_final: 0.7449 (m-80) REVERT: A 297 MET cc_start: 0.7858 (tmm) cc_final: 0.5408 (mtt) REVERT: A 420 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6632 (mp) REVERT: A 447 TYR cc_start: 0.7560 (OUTLIER) cc_final: 0.6529 (m-80) REVERT: A 471 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8045 (mp) outliers start: 31 outliers final: 27 residues processed: 94 average time/residue: 0.1362 time to fit residues: 18.6818 Evaluate side-chains 95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.682 ------------------------------------------------------------------------------- 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 330 SER 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 539 LEU 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 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 3 optimal weight: 0.2980 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 0.0870 chunk 54 optimal weight: 0.0270 chunk 9 optimal weight: 0.5980 overall best weight: 0.3416 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.182224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.158856 restraints weight = 6722.088| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.58 r_work: 0.3753 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3616 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6386 Z= 0.168 Angle : 0.529 8.914 8705 Z= 0.269 Chirality : 0.040 0.343 972 Planarity : 0.003 0.029 1053 Dihedral : 6.842 55.797 1105 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.12 % Allowed : 28.88 % Favored : 65.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.31), residues: 759 helix: 1.35 (0.26), residues: 373 sheet: 0.56 (0.53), residues: 114 loop : -0.85 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 234 HIS 0.001 0.000 HIS A 272 PHE 0.016 0.001 PHE A 603 TYR 0.018 0.001 TYR A 387 ARG 0.001 0.000 ARG A 644 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3364.64 seconds wall clock time: 60 minutes 26.51 seconds (3626.51 seconds total)