Starting phenix.real_space_refine on Sat May 10 04:39:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cy3_46005/05_2025/9cy3_46005.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cy3_46005/05_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_46005/05_2025/9cy3_46005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cy3_46005/05_2025/9cy3_46005.map" model { file = "/net/cci-nas-00/data/ceres_data/9cy3_46005/05_2025/9cy3_46005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cy3_46005/05_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 3.61, per 1000 atoms: 0.71 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: 1.33 Conformation dependent library (CDL) restraints added in 591.4 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: 0.53 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: 1.40 Time building geometry restraints manager: 1.48 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.860 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- 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 : 0.594 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: 0.1643 time to fit residues: 25.2410 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 : 0.576 ------------------------------------------------------------------------------- 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 = 0.4335 r_free = 0.4335 target = 0.208213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.183395 restraints weight = 6580.120| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 2.03 r_work: 0.3972 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3856 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1386 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 8.903 7067 Z= 0.297 Chirality : 0.041 0.134 786 Planarity : 0.004 0.044 867 Dihedral : 7.206 71.606 723 Min Nonbonded Distance : 2.551 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 4.85938 ( 855) SS BOND : bond 0.00150 ( 8) SS BOND : angle 0.96496 ( 16) covalent geometry : bond 0.00286 ( 5207) covalent geometry : angle 0.57052 ( 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 : 0.605 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7978 (tt) REVERT: A 97 ILE cc_start: 0.7659 (mt) cc_final: 0.7197 (mt) REVERT: A 348 GLN cc_start: 0.7426 (tp-100) cc_final: 0.7025 (tt0) REVERT: B 66 ASP cc_start: 0.7068 (m-30) cc_final: 0.6664 (m-30) outliers start: 11 outliers final: 6 residues processed: 102 average time/residue: 0.2105 time to fit residues: 28.4355 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 : 0.668 ------------------------------------------------------------------------------- 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: 0.4980 chunk 43 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 10 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.0270 overall best weight: 0.7840 ------------------------------------------------------------------------------- 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 = 0.4317 r_free = 0.4317 target = 0.205615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.179843 restraints weight = 6478.557| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 1.77 r_work: 0.3933 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5215 Z= 0.141 Angle : 0.573 10.306 7067 Z= 0.295 Chirality : 0.042 0.142 786 Planarity : 0.004 0.041 867 Dihedral : 6.258 58.230 723 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.14 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: 0.55 (0.32), residues: 637 helix: 1.38 (0.28), residues: 336 sheet: -0.70 (0.69), residues: 58 loop : -0.74 (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 0.03988 ( 287) hydrogen bonds : angle 4.79062 ( 855) SS BOND : bond 0.00180 ( 8) SS BOND : angle 0.78699 ( 16) covalent geometry : bond 0.00321 ( 5207) covalent geometry : angle 0.57240 ( 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 110 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8030 (tt) REVERT: A 574 PHE cc_start: 0.7338 (t80) cc_final: 0.7011 (t80) REVERT: B 58 TRP cc_start: 0.6507 (m100) cc_final: 0.5720 (m-90) REVERT: B 66 ASP cc_start: 0.7039 (m-30) cc_final: 0.6591 (m-30) outliers start: 10 outliers final: 7 residues processed: 105 average time/residue: 0.1625 time to fit residues: 22.7872 Evaluate side-chains 101 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.532 ------------------------------------------------------------------------------- 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: 5.9990 chunk 48 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 47 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4299 r_free = 0.4299 target = 0.204335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.178869 restraints weight = 6664.267| |-----------------------------------------------------------------------------| r_work (start): 0.4053 rms_B_bonded: 2.02 r_work: 0.3933 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3815 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5215 Z= 0.113 Angle : 0.527 6.994 7067 Z= 0.274 Chirality : 0.040 0.135 786 Planarity : 0.004 0.042 867 Dihedral : 5.910 57.124 723 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 15.87 % Favored : 81.73 % 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: 0.95 (0.33), residues: 637 helix: 1.71 (0.28), residues: 336 sheet: -0.67 (0.70), 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 0.007 0.001 HIS A 451 PHE 0.021 0.001 PHE A 175 TYR 0.024 0.001 TYR A 590 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 287) hydrogen bonds : angle 4.63652 ( 855) SS BOND : bond 0.00107 ( 8) SS BOND : angle 0.61063 ( 16) covalent geometry : bond 0.00246 ( 5207) covalent geometry : angle 0.52712 ( 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 118 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.594 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7438 (tm-30) cc_final: 0.7062 (tm-30) REVERT: A 348 GLN cc_start: 0.7404 (tp-100) cc_final: 0.6878 (tt0) REVERT: A 574 PHE cc_start: 0.7366 (t80) cc_final: 0.7011 (t80) REVERT: B 58 TRP cc_start: 0.6333 (m100) cc_final: 0.5521 (m-90) REVERT: B 66 ASP cc_start: 0.6911 (m-30) cc_final: 0.6554 (m-30) outliers start: 13 outliers final: 11 residues processed: 112 average time/residue: 0.1522 time to fit residues: 22.5521 Evaluate side-chains 104 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 385 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 577 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 2 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.0770 chunk 63 optimal weight: 0.0980 chunk 41 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.203881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.177397 restraints weight = 6539.632| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 1.84 r_work: 0.3927 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5215 Z= 0.115 Angle : 0.548 9.391 7067 Z= 0.282 Chirality : 0.041 0.174 786 Planarity : 0.004 0.042 867 Dihedral : 5.816 57.143 723 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.48 % Allowed : 18.45 % Favored : 80.07 % 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: 1.78 (0.28), residues: 337 sheet: -0.60 (0.70), residues: 58 loop : -0.45 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 PHE 0.033 0.001 PHE A 30 TYR 0.023 0.001 TYR A 590 ARG 0.004 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 287) hydrogen bonds : angle 4.64836 ( 855) SS BOND : bond 0.00134 ( 8) SS BOND : angle 0.59049 ( 16) covalent geometry : bond 0.00256 ( 5207) covalent geometry : angle 0.54802 ( 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 110 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 364 GLU cc_start: 0.7740 (tt0) cc_final: 0.7429 (tt0) REVERT: A 574 PHE cc_start: 0.7392 (t80) cc_final: 0.7188 (t80) REVERT: B 58 TRP cc_start: 0.6353 (m100) cc_final: 0.5606 (m-90) REVERT: B 66 ASP cc_start: 0.7027 (m-30) cc_final: 0.6689 (m-30) outliers start: 8 outliers final: 5 residues processed: 106 average time/residue: 0.1631 time to fit residues: 22.5297 Evaluate side-chains 97 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 461 SER 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: 0.0980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 40 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.4292 r_free = 0.4292 target = 0.203762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.177355 restraints weight = 6492.932| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.86 r_work: 0.3923 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5215 Z= 0.119 Angle : 0.553 9.295 7067 Z= 0.286 Chirality : 0.041 0.200 786 Planarity : 0.004 0.043 867 Dihedral : 5.685 56.866 723 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.85 % Allowed : 18.45 % 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: 1.12 (0.33), residues: 637 helix: 1.79 (0.28), residues: 336 sheet: -0.49 (0.71), residues: 58 loop : -0.38 (0.39), residues: 243 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 0.023 0.002 PHE A 30 TYR 0.023 0.001 TYR A 590 ARG 0.005 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 287) hydrogen bonds : angle 4.66903 ( 855) SS BOND : bond 0.00137 ( 8) SS BOND : angle 0.57798 ( 16) covalent geometry : bond 0.00268 ( 5207) covalent geometry : angle 0.55269 ( 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 110 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.576 Fit side-chains revert: symmetry clash REVERT: A 574 PHE cc_start: 0.7329 (t80) cc_final: 0.7042 (t80) REVERT: B 57 SER cc_start: 0.8416 (t) cc_final: 0.8185 (m) REVERT: B 66 ASP cc_start: 0.7060 (m-30) cc_final: 0.6681 (m-30) outliers start: 10 outliers final: 10 residues processed: 107 average time/residue: 0.1575 time to fit residues: 22.2230 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 : 0.562 ------------------------------------------------------------------------------- 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 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: 0.5980 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.0070 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.203789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.177315 restraints weight = 6487.157| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 1.82 r_work: 0.3931 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2622 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= 0.119 Angle : 0.570 10.318 7067 Z= 0.294 Chirality : 0.042 0.263 786 Planarity : 0.004 0.043 867 Dihedral : 5.594 56.183 723 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.85 % Allowed : 19.37 % Favored : 78.78 % 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: 1.22 (0.33), residues: 637 helix: 1.85 (0.28), residues: 335 sheet: -0.41 (0.72), residues: 58 loop : -0.29 (0.40), residues: 244 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 0.022 0.001 PHE A 175 TYR 0.022 0.001 TYR A 590 ARG 0.006 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 287) hydrogen bonds : angle 4.65169 ( 855) SS BOND : bond 0.00154 ( 8) SS BOND : angle 0.55685 ( 16) covalent geometry : bond 0.00271 ( 5207) covalent geometry : angle 0.57028 ( 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 107 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 346 LEU cc_start: 0.8192 (tt) cc_final: 0.7951 (tt) REVERT: A 364 GLU cc_start: 0.7797 (tt0) cc_final: 0.7474 (tt0) REVERT: A 574 PHE cc_start: 0.7248 (t80) cc_final: 0.6968 (t80) REVERT: B 66 ASP cc_start: 0.6965 (m-30) cc_final: 0.6611 (m-30) outliers start: 10 outliers final: 10 residues processed: 104 average time/residue: 0.1531 time to fit residues: 21.2806 Evaluate side-chains 103 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.560 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.0060 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 64 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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 = 0.4291 r_free = 0.4291 target = 0.203838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.177493 restraints weight = 6532.953| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.81 r_work: 0.3929 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3808 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5215 Z= 0.116 Angle : 0.560 9.424 7067 Z= 0.290 Chirality : 0.042 0.290 786 Planarity : 0.004 0.044 867 Dihedral : 5.536 55.894 723 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 19.19 % Favored : 78.41 % 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: 1.23 (0.33), residues: 637 helix: 1.87 (0.28), residues: 334 sheet: -0.33 (0.72), residues: 58 loop : -0.33 (0.40), residues: 245 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 268 TYR 0.023 0.001 TYR A 590 ARG 0.006 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 287) hydrogen bonds : angle 4.61005 ( 855) SS BOND : bond 0.00125 ( 8) SS BOND : angle 0.50993 ( 16) covalent geometry : bond 0.00261 ( 5207) covalent geometry : angle 0.55973 ( 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 112 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 99 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 335 ASN cc_start: 0.6898 (t0) cc_final: 0.6580 (t0) REVERT: A 346 LEU cc_start: 0.8187 (tt) cc_final: 0.7934 (tt) REVERT: A 364 GLU cc_start: 0.7840 (tt0) cc_final: 0.7503 (tt0) REVERT: A 401 LYS cc_start: 0.8544 (mmtp) cc_final: 0.8290 (mmmt) REVERT: B 57 SER cc_start: 0.8470 (t) cc_final: 0.8192 (m) REVERT: B 66 ASP cc_start: 0.6873 (m-30) cc_final: 0.6544 (m-30) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.1611 time to fit residues: 22.7840 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 : 0.578 ------------------------------------------------------------------------------- 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 458 TYR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 75 SER 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: 0.8980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4270 r_free = 0.4270 target = 0.201668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174907 restraints weight = 6486.800| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.81 r_work: 0.3905 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2827 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= 0.134 Angle : 0.584 9.026 7067 Z= 0.301 Chirality : 0.043 0.293 786 Planarity : 0.004 0.044 867 Dihedral : 5.576 56.366 723 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.58 % Allowed : 19.00 % Favored : 78.41 % 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: 1.63 (0.28), residues: 342 sheet: -0.41 (0.71), residues: 58 loop : -0.38 (0.40), residues: 237 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 0.020 0.002 PHE A 175 TYR 0.021 0.001 TYR A 590 ARG 0.006 0.001 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 287) hydrogen bonds : angle 4.75826 ( 855) SS BOND : bond 0.00148 ( 8) SS BOND : angle 0.55667 ( 16) covalent geometry : bond 0.00311 ( 5207) covalent geometry : angle 0.58372 ( 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 111 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 335 ASN cc_start: 0.6941 (t0) cc_final: 0.6687 (t0) REVERT: A 346 LEU cc_start: 0.8218 (tt) cc_final: 0.7967 (tt) REVERT: A 364 GLU cc_start: 0.7795 (tt0) cc_final: 0.7464 (tt0) REVERT: B 66 ASP cc_start: 0.6882 (m-30) cc_final: 0.6513 (m-30) outliers start: 14 outliers final: 13 residues processed: 106 average time/residue: 0.1436 time to fit residues: 20.2853 Evaluate side-chains 108 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 543 LEU Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 75 SER 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 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 38 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4266 r_free = 0.4266 target = 0.201321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.174614 restraints weight = 6433.437| |-----------------------------------------------------------------------------| r_work (start): 0.4003 rms_B_bonded: 1.81 r_work: 0.3902 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2892 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= 0.134 Angle : 0.591 9.100 7067 Z= 0.305 Chirality : 0.043 0.302 786 Planarity : 0.004 0.044 867 Dihedral : 5.592 56.129 723 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.21 % Allowed : 19.56 % 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: 1.00 (0.33), residues: 637 helix: 1.70 (0.28), residues: 336 sheet: -0.43 (0.71), residues: 58 loop : -0.48 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.007 0.001 HIS A 451 PHE 0.021 0.002 PHE A 413 TYR 0.021 0.001 TYR A 590 ARG 0.007 0.001 ARG B 103 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 287) hydrogen bonds : angle 4.77524 ( 855) SS BOND : bond 0.00178 ( 8) SS BOND : angle 0.55576 ( 16) covalent geometry : bond 0.00310 ( 5207) covalent geometry : angle 0.59076 ( 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 108 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 346 LEU cc_start: 0.8220 (tt) cc_final: 0.7964 (tt) REVERT: A 364 GLU cc_start: 0.7821 (tt0) cc_final: 0.7503 (tt0) REVERT: A 467 GLU cc_start: 0.6642 (mt-10) cc_final: 0.6238 (mp0) REVERT: B 66 ASP cc_start: 0.6963 (m-30) cc_final: 0.6579 (m-30) outliers start: 12 outliers final: 11 residues processed: 103 average time/residue: 0.1578 time to fit residues: 21.5880 Evaluate side-chains 105 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 543 LEU Chi-restraints excluded: chain A residue 577 MET Chi-restraints excluded: chain B residue 26 CYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 75 SER 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: 0.2980 chunk 45 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 0.0060 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 60 optimal weight: 0.6980 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.205290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.178818 restraints weight = 6583.252| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 1.85 r_work: 0.3948 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5215 Z= 0.107 Angle : 0.563 9.259 7067 Z= 0.288 Chirality : 0.042 0.320 786 Planarity : 0.004 0.044 867 Dihedral : 5.406 54.863 723 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.03 % Allowed : 19.56 % Favored : 78.41 % 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: 1.25 (0.34), residues: 637 helix: 1.90 (0.28), residues: 336 sheet: -0.21 (0.73), residues: 58 loop : -0.37 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 PHE 0.021 0.001 PHE A 175 TYR 0.024 0.001 TYR A 590 ARG 0.006 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 287) hydrogen bonds : angle 4.53132 ( 855) SS BOND : bond 0.00117 ( 8) SS BOND : angle 0.59851 ( 16) covalent geometry : bond 0.00231 ( 5207) covalent geometry : angle 0.56336 ( 7051) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3132.47 seconds wall clock time: 55 minutes 6.27 seconds (3306.27 seconds total)