Starting phenix.real_space_refine on Sun Apr 27 08:06:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cy3_46005/04_2025/9cy3_46005.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cy3_46005/04_2025/9cy3_46005.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cy3_46005/04_2025/9cy3_46005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cy3_46005/04_2025/9cy3_46005.map" model { file = "/net/cci-nas-00/data/ceres_data/9cy3_46005/04_2025/9cy3_46005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cy3_46005/04_2025/9cy3_46005.cif" } resolution = 3.2 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= 0.026 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: 5 Type Number sf(0) Gaussians S 38 5.16 5 C 3327 2.51 5 N 815 2.21 5 O 897 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 5078 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4125 Classifications: {'peptide': 533} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 19, 'TRANS': 513} Chain breaks: 6 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 912 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'117': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.69, per 1000 atoms: 0.73 Number of scatterers: 5078 At special positions: 0 Unit cell: (57.148, 104.405, 106.603, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 F 1 9.00 O 897 8.00 N 815 7.00 C 3327 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 463 " distance=2.02 Simple disulfide: pdb=" SG CYS A 430 " - pdb=" SG CYS A 530 " distance=2.03 Simple disulfide: pdb=" SG CYS A 459 " - pdb=" SG CYS A 506 " distance=2.03 Simple disulfide: pdb=" SG CYS A 465 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 524 " distance=2.03 Simple disulfide: pdb=" SG CYS A 489 " - pdb=" SG CYS A 504 " distance=2.03 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 100 " 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 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 571.6 milliseconds 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 5 sheets defined 56.7% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 26 through 51 removed outlier: 3.645A pdb=" N PHE A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 60 removed outlier: 3.542A pdb=" N ILE A 55 " --> pdb=" O SER A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 88 removed outlier: 4.328A pdb=" N PHE A 73 " --> pdb=" O ILE A 69 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU A 74 " --> pdb=" O ASP A 70 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL A 80 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N VAL A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 113 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 170 through 186 removed outlier: 3.700A pdb=" N VAL A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 198 Processing helix chain 'A' and resid 203 through 216 removed outlier: 4.151A pdb=" N LEU A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.741A pdb=" N ILE A 221 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.574A pdb=" N ILE A 245 " --> pdb=" O LEU A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 278 removed outlier: 3.735A pdb=" N ILE A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Proline residue: A 275 - end of helix removed outlier: 4.016A pdb=" N PHE A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 334 Processing helix chain 'A' and resid 335 through 367 removed outlier: 4.035A pdb=" N TYR A 358 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N PHE A 360 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS A 361 " --> pdb=" O THR A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 400 removed outlier: 3.592A pdb=" N ILE A 385 " --> pdb=" O ILE A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.644A pdb=" N ILE A 428 " --> pdb=" O TYR A 425 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LEU A 429 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 552 removed outlier: 3.818A pdb=" N ARG A 532 " --> pdb=" O ASP A 528 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LYS A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 563 removed outlier: 3.901A pdb=" N ILE A 559 " --> pdb=" O HIS A 555 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 560 " --> pdb=" O VAL A 556 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LYS A 561 " --> pdb=" O MET A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 583 Processing helix chain 'A' and resid 585 through 597 removed outlier: 3.562A pdb=" N ILE A 589 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 651 removed outlier: 3.972A pdb=" N SER A 629 " --> pdb=" O TYR A 625 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 Processing sheet with id=AA1, first strand: chain 'A' and resid 480 through 481 removed outlier: 3.623A pdb=" N CYS A 474 " --> pdb=" O HIS A 520 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 599 through 601 removed outlier: 3.502A pdb=" N ILE A 600 " --> pdb=" O THR A 615 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N THR A 615 " --> pdb=" O ILE A 600 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 7 through 11 Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.545A pdb=" N GLU B 63 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP B 40 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA B 54 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET B 38 " --> pdb=" O ALA B 54 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 64 removed outlier: 3.545A pdb=" N GLU B 63 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N TRP B 40 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ALA B 54 " --> pdb=" O MET B 38 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET B 38 " --> pdb=" O ALA B 54 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR B 113 " --> pdb=" O TYR B 98 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 855 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: 1.78 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1512 1.34 - 1.46: 1388 1.46 - 1.58: 2250 1.58 - 1.71: 0 1.71 - 1.83: 57 Bond restraints: 5207 Sorted by residual: bond pdb=" C VAL A 189 " pdb=" N PRO A 190 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.17e+00 bond pdb=" C ILE A 383 " pdb=" N PRO A 384 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.58e+00 bond pdb=" C ARG A 93 " pdb=" N PRO A 94 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.23e-02 6.61e+03 3.43e+00 bond pdb=" C ILE A 274 " pdb=" N PRO A 275 " ideal model delta sigma weight residual 1.337 1.356 -0.020 1.11e-02 8.12e+03 3.11e+00 bond pdb=" N ILE A 274 " pdb=" CA ILE A 274 " ideal model delta sigma weight residual 1.463 1.483 -0.020 1.20e-02 6.94e+03 2.85e+00 ... (remaining 5202 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.55: 6839 2.55 - 5.11: 178 5.11 - 7.66: 25 7.66 - 10.22: 7 10.22 - 12.77: 2 Bond angle restraints: 7051 Sorted by residual: angle pdb=" C ALA B 18 " pdb=" CA ALA B 18 " pdb=" CB ALA B 18 " ideal model delta sigma weight residual 115.79 110.63 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" CB MET A 48 " pdb=" CG MET A 48 " pdb=" SD MET A 48 " ideal model delta sigma weight residual 112.70 125.47 -12.77 3.00e+00 1.11e-01 1.81e+01 angle pdb=" N VAL B 115 " pdb=" CA VAL B 115 " pdb=" C VAL B 115 " ideal model delta sigma weight residual 109.34 101.91 7.43 2.08e+00 2.31e-01 1.28e+01 angle pdb=" C VAL B 115 " pdb=" CA VAL B 115 " pdb=" CB VAL B 115 " ideal model delta sigma weight residual 111.29 117.14 -5.85 1.64e+00 3.72e-01 1.27e+01 angle pdb=" CA TYR A 590 " pdb=" CB TYR A 590 " pdb=" CG TYR A 590 " ideal model delta sigma weight residual 113.90 120.31 -6.41 1.80e+00 3.09e-01 1.27e+01 ... (remaining 7046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.61: 2818 22.61 - 45.22: 176 45.22 - 67.83: 16 67.83 - 90.44: 5 90.44 - 113.04: 3 Dihedral angle restraints: 3018 sinusoidal: 1153 harmonic: 1865 Sorted by residual: dihedral pdb=" CB CYS A 474 " pdb=" SG CYS A 474 " pdb=" SG CYS A 524 " pdb=" CB CYS A 524 " ideal model delta sinusoidal sigma weight residual 93.00 140.47 -47.47 1 1.00e+01 1.00e-02 3.11e+01 dihedral pdb=" CA GLY A 551 " pdb=" C GLY A 551 " pdb=" N GLY A 552 " pdb=" CA GLY A 552 " ideal model delta harmonic sigma weight residual 180.00 159.25 20.75 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA ILE A 196 " pdb=" C ILE A 196 " pdb=" N ASP A 197 " pdb=" CA ASP A 197 " ideal model delta harmonic sigma weight residual -180.00 -160.32 -19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 3015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 568 0.051 - 0.102: 150 0.102 - 0.152: 52 0.152 - 0.203: 14 0.203 - 0.254: 2 Chirality restraints: 786 Sorted by residual: chirality pdb=" CB VAL B 102 " pdb=" CA VAL B 102 " pdb=" CG1 VAL B 102 " pdb=" CG2 VAL B 102 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB VAL A 448 " pdb=" CA VAL A 448 " pdb=" CG1 VAL A 448 " pdb=" CG2 VAL A 448 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE A 600 " pdb=" CA ILE A 600 " pdb=" CG1 ILE A 600 " pdb=" CG2 ILE A 600 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.67e-01 ... (remaining 783 not shown) Planarity restraints: 867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 117 A 701 " 0.010 2.00e-02 2.50e+03 4.92e-02 6.06e+01 pdb=" C11 117 A 701 " 0.006 2.00e-02 2.50e+03 pdb=" C12 117 A 701 " 0.086 2.00e-02 2.50e+03 pdb=" C18 117 A 701 " -0.076 2.00e-02 2.50e+03 pdb=" C7 117 A 701 " 0.039 2.00e-02 2.50e+03 pdb=" C8 117 A 701 " 0.006 2.00e-02 2.50e+03 pdb=" C81 117 A 701 " -0.096 2.00e-02 2.50e+03 pdb=" C9 117 A 701 " 0.008 2.00e-02 2.50e+03 pdb=" C91 117 A 701 " 0.007 2.00e-02 2.50e+03 pdb=" N1 117 A 701 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C8 117 A 701 " -0.043 2.00e-02 2.50e+03 2.37e-02 1.13e+01 pdb=" C81 117 A 701 " 0.018 2.00e-02 2.50e+03 pdb=" C82 117 A 701 " 0.017 2.00e-02 2.50e+03 pdb=" C83 117 A 701 " 0.011 2.00e-02 2.50e+03 pdb=" C84 117 A 701 " 0.007 2.00e-02 2.50e+03 pdb=" C85 117 A 701 " 0.011 2.00e-02 2.50e+03 pdb=" C86 117 A 701 " 0.017 2.00e-02 2.50e+03 pdb=" F1 117 A 701 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 68 " 0.021 2.00e-02 2.50e+03 1.96e-02 6.72e+00 pdb=" CG PHE A 68 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 68 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 68 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 68 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 68 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 68 " -0.000 2.00e-02 2.50e+03 ... (remaining 864 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 1665 2.84 - 3.36: 4742 3.36 - 3.87: 8236 3.87 - 4.39: 9469 4.39 - 4.90: 16480 Nonbonded interactions: 40592 Sorted by model distance: nonbonded pdb=" OG1 THR A 441 " pdb=" OD1 ASP A 443 " model vdw 2.331 3.040 nonbonded pdb=" O ILE A 353 " pdb=" OG1 THR A 357 " model vdw 2.363 3.040 nonbonded pdb=" OG SER B 56 " pdb=" N SER B 57 " model vdw 2.379 3.120 nonbonded pdb=" O ASP A 241 " pdb=" OG1 THR A 244 " model vdw 2.382 3.040 nonbonded pdb=" O ASN B 34 " pdb=" OG SER B 57 " model vdw 2.392 3.040 ... (remaining 40587 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: 0.770 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.660 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 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:3.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 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 : 0.005 0.062 5215 Z= 0.229 Angle : 0.961 12.774 7067 Z= 0.513 Chirality : 0.055 0.254 786 Planarity : 0.008 0.050 867 Dihedral : 14.280 113.045 1810 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.29), residues: 637 helix: -0.43 (0.24), residues: 316 sheet: -0.98 (0.67), residues: 65 loop : -1.23 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 171 HIS 0.018 0.003 HIS A 451 PHE 0.045 0.002 PHE A 68 TYR 0.041 0.003 TYR A 338 ARG 0.012 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.14773 ( 287) hydrogen bonds : angle 6.96854 ( 855) SS BOND : bond 0.00306 ( 8) SS BOND : angle 1.35890 ( 16) covalent geometry : bond 0.00484 ( 5207) covalent geometry : angle 0.96007 ( 7051) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: A 97 ILE cc_start: 0.7394 (mt) cc_final: 0.6957 (mt) REVERT: A 348 GLN cc_start: 0.7069 (tp-100) cc_final: 0.6715 (tt0) REVERT: A 402 LEU cc_start: 0.7653 (mt) cc_final: 0.7377 (mt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1784 time to fit residues: 27.3847 Evaluate side-chains 90 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.208220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183414 restraints weight = 6580.091| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 2.03 r_work: 0.3972 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3858 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5215 Z= 0.130 Angle : 0.572 8.904 7067 Z= 0.297 Chirality : 0.041 0.133 786 Planarity : 0.004 0.044 867 Dihedral : 7.204 71.558 723 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.03 % Allowed : 9.04 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.32), residues: 637 helix: 0.94 (0.27), residues: 335 sheet: -0.72 (0.71), residues: 58 loop : -0.92 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 40 HIS 0.008 0.001 HIS A 451 PHE 0.016 0.002 PHE A 329 TYR 0.024 0.001 TYR A 338 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 287) hydrogen bonds : angle 4.85919 ( 855) SS BOND : bond 0.00149 ( 8) SS BOND : angle 0.96428 ( 16) covalent geometry : bond 0.00286 ( 5207) covalent geometry : angle 0.57048 ( 7051) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7974 (tt) REVERT: A 97 ILE cc_start: 0.7660 (mt) cc_final: 0.7199 (mt) REVERT: A 348 GLN cc_start: 0.7424 (tp-100) cc_final: 0.7021 (tt0) REVERT: B 66 ASP cc_start: 0.7051 (m-30) cc_final: 0.6648 (m-30) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.1714 time to fit residues: 23.7567 Evaluate side-chains 96 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 41 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.0980 chunk 43 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 21 optimal weight: 0.0010 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.205424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.180394 restraints weight = 6612.556| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.03 r_work: 0.3931 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3810 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5215 Z= 0.140 Angle : 0.571 10.280 7067 Z= 0.294 Chirality : 0.042 0.140 786 Planarity : 0.004 0.041 867 Dihedral : 6.248 58.098 723 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.85 % Allowed : 12.55 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.32), residues: 637 helix: 1.40 (0.28), residues: 336 sheet: -0.68 (0.70), residues: 58 loop : -0.73 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 171 HIS 0.008 0.001 HIS A 451 PHE 0.019 0.002 PHE A 413 TYR 0.024 0.001 TYR A 590 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 287) hydrogen bonds : angle 4.77712 ( 855) SS BOND : bond 0.00185 ( 8) SS BOND : angle 0.77944 ( 16) covalent geometry : bond 0.00317 ( 5207) covalent geometry : angle 0.57051 ( 7051) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8084 (tt) REVERT: A 574 PHE cc_start: 0.7317 (t80) cc_final: 0.6997 (t80) REVERT: B 58 TRP cc_start: 0.6487 (m100) cc_final: 0.5701 (m-90) REVERT: B 66 ASP cc_start: 0.7084 (m-30) cc_final: 0.6647 (m-30) outliers start: 10 outliers final: 7 residues processed: 107 average time/residue: 0.2213 time to fit residues: 32.1814 Evaluate side-chains 103 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 95 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 40 optimal weight: 0.0170 chunk 48 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.0030 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 4 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 overall best weight: 0.3428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 544 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.205833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.180546 restraints weight = 6684.787| |-----------------------------------------------------------------------------| r_work (start): 0.4070 rms_B_bonded: 2.03 r_work: 0.3951 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3833 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5215 Z= 0.104 Angle : 0.515 6.797 7067 Z= 0.267 Chirality : 0.040 0.146 786 Planarity : 0.003 0.042 867 Dihedral : 5.869 56.781 723 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.66 % Allowed : 16.79 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.33), residues: 637 helix: 1.78 (0.28), residues: 336 sheet: -0.55 (0.71), residues: 58 loop : -0.52 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 PHE 0.020 0.001 PHE A 68 TYR 0.024 0.001 TYR A 590 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 287) hydrogen bonds : angle 4.56886 ( 855) SS BOND : bond 0.00111 ( 8) SS BOND : angle 0.58485 ( 16) covalent geometry : bond 0.00220 ( 5207) covalent geometry : angle 0.51486 ( 7051) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7132 (tm-30) REVERT: A 348 GLN cc_start: 0.7342 (tp-100) cc_final: 0.6795 (tt0) REVERT: A 574 PHE cc_start: 0.7329 (t80) cc_final: 0.6950 (t80) REVERT: A 640 TYR cc_start: 0.7408 (m-80) cc_final: 0.7194 (m-80) REVERT: B 58 TRP cc_start: 0.6334 (m100) cc_final: 0.5519 (m-90) REVERT: B 66 ASP cc_start: 0.6965 (m-30) cc_final: 0.6615 (m-30) outliers start: 9 outliers final: 6 residues processed: 110 average time/residue: 0.1859 time to fit residues: 27.5354 Evaluate side-chains 100 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.200312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.174938 restraints weight = 6545.744| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.98 r_work: 0.3882 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5215 Z= 0.158 Angle : 0.583 7.020 7067 Z= 0.304 Chirality : 0.042 0.168 786 Planarity : 0.004 0.040 867 Dihedral : 6.003 58.145 723 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.85 % Allowed : 17.53 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.33), residues: 637 helix: 1.55 (0.28), residues: 338 sheet: -0.87 (0.67), residues: 58 loop : -0.53 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 PHE 0.034 0.002 PHE A 30 TYR 0.020 0.002 TYR A 590 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 287) hydrogen bonds : angle 4.87020 ( 855) SS BOND : bond 0.00230 ( 8) SS BOND : angle 0.74329 ( 16) covalent geometry : bond 0.00369 ( 5207) covalent geometry : angle 0.58287 ( 7051) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7314 (tm-30) cc_final: 0.6910 (tm-30) REVERT: A 346 LEU cc_start: 0.8254 (tt) cc_final: 0.8005 (tt) REVERT: B 58 TRP cc_start: 0.6502 (m100) cc_final: 0.5664 (m-90) REVERT: B 66 ASP cc_start: 0.7187 (m-30) cc_final: 0.6809 (m-30) outliers start: 10 outliers final: 8 residues processed: 102 average time/residue: 0.2061 time to fit residues: 28.5026 Evaluate side-chains 99 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.201053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.173866 restraints weight = 6503.107| |-----------------------------------------------------------------------------| r_work (start): 0.3991 rms_B_bonded: 1.84 r_work: 0.3888 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3771 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5215 Z= 0.139 Angle : 0.562 8.442 7067 Z= 0.292 Chirality : 0.041 0.154 786 Planarity : 0.004 0.040 867 Dihedral : 5.896 57.572 723 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.40 % Allowed : 17.90 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.33), residues: 637 helix: 1.62 (0.28), residues: 337 sheet: -0.86 (0.67), residues: 58 loop : -0.48 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 PHE 0.024 0.002 PHE A 30 TYR 0.022 0.001 TYR A 590 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03692 ( 287) hydrogen bonds : angle 4.85369 ( 855) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.59631 ( 16) covalent geometry : bond 0.00323 ( 5207) covalent geometry : angle 0.56142 ( 7051) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 346 LEU cc_start: 0.8234 (tt) cc_final: 0.7989 (tt) REVERT: A 574 PHE cc_start: 0.7170 (t80) cc_final: 0.6895 (t80) REVERT: B 66 ASP cc_start: 0.6980 (m-30) cc_final: 0.6593 (m-30) outliers start: 13 outliers final: 12 residues processed: 108 average time/residue: 0.1962 time to fit residues: 28.5620 Evaluate side-chains 107 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 560 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 53 optimal weight: 0.0040 chunk 14 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.201802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.175146 restraints weight = 6471.693| |-----------------------------------------------------------------------------| r_work (start): 0.4004 rms_B_bonded: 1.80 r_work: 0.3907 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5215 Z= 0.121 Angle : 0.567 10.633 7067 Z= 0.294 Chirality : 0.041 0.128 786 Planarity : 0.004 0.041 867 Dihedral : 5.789 57.087 723 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.40 % Allowed : 18.63 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.33), residues: 637 helix: 1.71 (0.28), residues: 337 sheet: -0.73 (0.69), residues: 58 loop : -0.48 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 PHE 0.021 0.001 PHE A 30 TYR 0.022 0.001 TYR A 590 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03578 ( 287) hydrogen bonds : angle 4.74283 ( 855) SS BOND : bond 0.00170 ( 8) SS BOND : angle 0.57721 ( 16) covalent geometry : bond 0.00276 ( 5207) covalent geometry : angle 0.56701 ( 7051) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 346 LEU cc_start: 0.8211 (tt) cc_final: 0.7961 (tt) REVERT: B 57 SER cc_start: 0.8468 (t) cc_final: 0.8160 (m) REVERT: B 66 ASP cc_start: 0.6978 (m-30) cc_final: 0.6636 (m-30) outliers start: 13 outliers final: 11 residues processed: 108 average time/residue: 0.2174 time to fit residues: 31.4948 Evaluate side-chains 107 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 51 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.201705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.174602 restraints weight = 6544.690| |-----------------------------------------------------------------------------| r_work (start): 0.3999 rms_B_bonded: 1.85 r_work: 0.3901 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3783 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5215 Z= 0.122 Angle : 0.570 10.767 7067 Z= 0.293 Chirality : 0.041 0.220 786 Planarity : 0.004 0.040 867 Dihedral : 5.670 56.841 723 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.77 % Allowed : 18.63 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.33), residues: 637 helix: 1.73 (0.28), residues: 338 sheet: -0.58 (0.70), residues: 58 loop : -0.43 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 PHE 0.023 0.001 PHE A 413 TYR 0.022 0.001 TYR A 590 ARG 0.006 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 287) hydrogen bonds : angle 4.72372 ( 855) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.56643 ( 16) covalent geometry : bond 0.00279 ( 5207) covalent geometry : angle 0.56965 ( 7051) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 346 LEU cc_start: 0.8218 (tt) cc_final: 0.7967 (tt) REVERT: B 57 SER cc_start: 0.8440 (t) cc_final: 0.8130 (m) REVERT: B 66 ASP cc_start: 0.7033 (m-30) cc_final: 0.6678 (m-30) outliers start: 15 outliers final: 15 residues processed: 109 average time/residue: 0.2138 time to fit residues: 30.2963 Evaluate side-chains 109 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 458 TYR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 19 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.201348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.174342 restraints weight = 6478.586| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.83 r_work: 0.3895 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3774 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 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 0.048 5215 Z= 0.126 Angle : 0.582 10.469 7067 Z= 0.302 Chirality : 0.042 0.274 786 Planarity : 0.004 0.041 867 Dihedral : 5.608 56.557 723 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.32 % Allowed : 18.45 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.33), residues: 637 helix: 1.73 (0.28), residues: 337 sheet: -0.53 (0.70), residues: 58 loop : -0.47 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 PHE 0.024 0.002 PHE A 268 TYR 0.022 0.001 TYR A 590 ARG 0.006 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03597 ( 287) hydrogen bonds : angle 4.71475 ( 855) SS BOND : bond 0.00141 ( 8) SS BOND : angle 0.60213 ( 16) covalent geometry : bond 0.00288 ( 5207) covalent geometry : angle 0.58198 ( 7051) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.761 Fit side-chains REVERT: A 346 LEU cc_start: 0.8203 (tt) cc_final: 0.7954 (tt) REVERT: A 467 GLU cc_start: 0.6658 (mt-10) cc_final: 0.5932 (tm-30) REVERT: B 57 SER cc_start: 0.8500 (t) cc_final: 0.8201 (m) REVERT: B 66 ASP cc_start: 0.7071 (m-30) cc_final: 0.6697 (m-30) outliers start: 18 outliers final: 16 residues processed: 107 average time/residue: 0.2468 time to fit residues: 35.4522 Evaluate side-chains 108 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 46 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 53 optimal weight: 0.0050 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 516 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.202522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.175889 restraints weight = 6430.023| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.81 r_work: 0.3915 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5215 Z= 0.118 Angle : 0.577 9.963 7067 Z= 0.298 Chirality : 0.042 0.316 786 Planarity : 0.004 0.040 867 Dihedral : 5.488 55.934 723 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.14 % Allowed : 19.19 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.33), residues: 637 helix: 1.68 (0.28), residues: 342 sheet: -0.43 (0.70), residues: 58 loop : -0.38 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 171 HIS 0.007 0.001 HIS A 451 PHE 0.023 0.001 PHE A 413 TYR 0.023 0.001 TYR A 590 ARG 0.006 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03485 ( 287) hydrogen bonds : angle 4.63599 ( 855) SS BOND : bond 0.00142 ( 8) SS BOND : angle 0.54122 ( 16) covalent geometry : bond 0.00265 ( 5207) covalent geometry : angle 0.57704 ( 7051) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1274 Ramachandran restraints generated. 637 Oldfield, 0 Emsley, 637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.640 Fit side-chains REVERT: A 346 LEU cc_start: 0.8192 (tt) cc_final: 0.7939 (tt) REVERT: A 467 GLU cc_start: 0.6609 (mt-10) cc_final: 0.5947 (tm-30) REVERT: B 57 SER cc_start: 0.8497 (t) cc_final: 0.8229 (m) REVERT: B 66 ASP cc_start: 0.7047 (m-30) cc_final: 0.6694 (m-30) outliers start: 17 outliers final: 14 residues processed: 109 average time/residue: 0.2258 time to fit residues: 33.4277 Evaluate side-chains 106 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 202 GLU Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 88 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 47 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 4 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 21 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.202661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175638 restraints weight = 6583.912| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 1.85 r_work: 0.3912 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3790 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5215 Z= 0.117 Angle : 0.577 9.964 7067 Z= 0.298 Chirality : 0.042 0.311 786 Planarity : 0.004 0.041 867 Dihedral : 5.407 55.412 723 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.77 % Allowed : 19.93 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.33), residues: 637 helix: 1.68 (0.28), residues: 342 sheet: -0.29 (0.72), residues: 58 loop : -0.38 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 171 HIS 0.007 0.001 HIS A 451 PHE 0.023 0.001 PHE A 413 TYR 0.023 0.001 TYR A 590 ARG 0.007 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03460 ( 287) hydrogen bonds : angle 4.62759 ( 855) SS BOND : bond 0.00118 ( 8) SS BOND : angle 0.54968 ( 16) covalent geometry : bond 0.00266 ( 5207) covalent geometry : angle 0.57706 ( 7051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3593.00 seconds wall clock time: 66 minutes 20.51 seconds (3980.51 seconds total)