Starting phenix.real_space_refine on Wed Sep 17 05:22:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cy3_46005/09_2025/9cy3_46005.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cy3_46005/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cy3_46005/09_2025/9cy3_46005.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cy3_46005/09_2025/9cy3_46005.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cy3_46005/09_2025/9cy3_46005.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cy3_46005/09_2025/9cy3_46005.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'ARG:plan': 1, 'TYR: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: 1.38, per 1000 atoms: 0.27 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: 0.40 Conformation dependent library (CDL) restraints added in 221.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.13 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: 0.70 Time building geometry restraints manager: 0.47 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: 0.970 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.670 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.012 0.001 ARG B 49 TYR 0.041 0.003 TYR A 338 PHE 0.045 0.002 PHE A 68 TRP 0.013 0.001 TRP A 171 HIS 0.018 0.003 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00484 ( 5207) covalent geometry : angle 0.96007 ( 7051) SS BOND : bond 0.00306 ( 8) SS BOND : angle 1.35890 ( 16) hydrogen bonds : bond 0.14773 ( 287) hydrogen bonds : angle 6.96854 ( 855) *********************** 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 : 0.167 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: 0.0651 time to fit residues: 10.0644 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 : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.4303 r_free = 0.4303 target = 0.205079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.179792 restraints weight = 6647.502| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 2.01 r_work: 0.3936 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3819 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5215 Z= 0.160 Angle : 0.605 9.146 7067 Z= 0.315 Chirality : 0.043 0.126 786 Planarity : 0.004 0.041 867 Dihedral : 6.998 64.478 723 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.85 % Allowed : 9.78 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.31), residues: 637 helix: 0.85 (0.27), residues: 335 sheet: -0.80 (0.71), residues: 58 loop : -0.95 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 42 TYR 0.024 0.002 TYR A 338 PHE 0.020 0.002 PHE A 329 TRP 0.009 0.001 TRP B 40 HIS 0.008 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 5207) covalent geometry : angle 0.60370 ( 7051) SS BOND : bond 0.00348 ( 8) SS BOND : angle 1.01399 ( 16) hydrogen bonds : bond 0.04239 ( 287) hydrogen bonds : angle 4.97869 ( 855) *********************** 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 113 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8134 (tt) REVERT: A 348 GLN cc_start: 0.7389 (tp-100) cc_final: 0.6892 (tt0) REVERT: A 574 PHE cc_start: 0.7378 (t80) cc_final: 0.7165 (t80) REVERT: B 64 TYR cc_start: 0.8345 (m-80) cc_final: 0.8063 (m-80) REVERT: B 66 ASP cc_start: 0.7111 (m-30) cc_final: 0.6675 (m-30) outliers start: 10 outliers final: 6 residues processed: 108 average time/residue: 0.0660 time to fit residues: 9.4393 Evaluate side-chains 100 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 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 12 optimal weight: 0.7980 chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 0.0020 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 541 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.203729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.177033 restraints weight = 6574.109| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.86 r_work: 0.3926 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.1896 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= 0.124 Angle : 0.545 6.606 7067 Z= 0.282 Chirality : 0.041 0.149 786 Planarity : 0.004 0.042 867 Dihedral : 6.115 56.607 723 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.66 % Allowed : 13.65 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.32), residues: 637 helix: 1.44 (0.28), residues: 336 sheet: -0.65 (0.71), residues: 58 loop : -0.76 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 49 TYR 0.025 0.001 TYR A 590 PHE 0.022 0.001 PHE A 413 TRP 0.007 0.001 TRP B 40 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 5207) covalent geometry : angle 0.54436 ( 7051) SS BOND : bond 0.00150 ( 8) SS BOND : angle 0.75036 ( 16) hydrogen bonds : bond 0.03877 ( 287) hydrogen bonds : angle 4.72430 ( 855) *********************** 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: 9 poor density : 103 time to evaluate : 0.215 Fit side-chains revert: symmetry clash REVERT: A 96 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8054 (tt) REVERT: A 574 PHE cc_start: 0.7418 (t80) cc_final: 0.7076 (t80) REVERT: B 58 TRP cc_start: 0.6345 (m100) cc_final: 0.5576 (m-90) REVERT: B 66 ASP cc_start: 0.6936 (m-30) cc_final: 0.6578 (m-30) outliers start: 9 outliers final: 5 residues processed: 109 average time/residue: 0.0688 time to fit residues: 9.9651 Evaluate side-chains 99 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 93 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 561 LYS Chi-restraints excluded: chain A residue 620 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 0.0060 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.3980 chunk 62 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.204182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.177571 restraints weight = 6583.329| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.85 r_work: 0.3928 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5215 Z= 0.113 Angle : 0.539 10.432 7067 Z= 0.277 Chirality : 0.040 0.134 786 Planarity : 0.004 0.042 867 Dihedral : 5.876 56.788 723 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.85 % Allowed : 15.50 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.33), residues: 637 helix: 1.66 (0.28), residues: 336 sheet: -0.54 (0.71), residues: 58 loop : -0.58 (0.38), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 49 TYR 0.024 0.001 TYR A 590 PHE 0.030 0.002 PHE A 30 TRP 0.010 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 5207) covalent geometry : angle 0.53859 ( 7051) SS BOND : bond 0.00125 ( 8) SS BOND : angle 0.60634 ( 16) hydrogen bonds : bond 0.03624 ( 287) hydrogen bonds : angle 4.63436 ( 855) *********************** 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: 10 poor density : 105 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7409 (tm-30) cc_final: 0.7051 (tm-30) REVERT: A 574 PHE cc_start: 0.7489 (t80) cc_final: 0.7129 (t80) REVERT: B 58 TRP cc_start: 0.6351 (m100) cc_final: 0.5564 (m-90) REVERT: B 66 ASP cc_start: 0.6858 (m-30) cc_final: 0.6542 (m-30) outliers start: 10 outliers final: 6 residues processed: 111 average time/residue: 0.0697 time to fit residues: 10.2577 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 : 0.232 ------------------------------------------------------------------------------- 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 359 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.202052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.176523 restraints weight = 6616.573| |-----------------------------------------------------------------------------| r_work (start): 0.4022 rms_B_bonded: 2.01 r_work: 0.3897 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3776 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2372 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= 0.139 Angle : 0.571 11.685 7067 Z= 0.294 Chirality : 0.041 0.131 786 Planarity : 0.004 0.042 867 Dihedral : 5.880 57.325 723 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.66 % Allowed : 18.08 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.33), residues: 637 helix: 1.63 (0.28), residues: 337 sheet: -0.69 (0.70), residues: 58 loop : -0.48 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 42 TYR 0.022 0.001 TYR A 590 PHE 0.021 0.002 PHE A 30 TRP 0.009 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5207) covalent geometry : angle 0.57033 ( 7051) SS BOND : bond 0.00165 ( 8) SS BOND : angle 0.65433 ( 16) hydrogen bonds : bond 0.03702 ( 287) hydrogen bonds : angle 4.78189 ( 855) *********************** 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 106 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 364 GLU cc_start: 0.7714 (tt0) cc_final: 0.7392 (tt0) REVERT: B 58 TRP cc_start: 0.6476 (m100) cc_final: 0.5627 (m-90) REVERT: B 66 ASP cc_start: 0.7091 (m-30) cc_final: 0.6730 (m-30) outliers start: 9 outliers final: 7 residues processed: 102 average time/residue: 0.0698 time to fit residues: 9.4747 Evaluate side-chains 99 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.185 ------------------------------------------------------------------------------- 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 359 VAL 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 8 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 19 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 54 optimal weight: 0.0020 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- 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 = 0.4278 r_free = 0.4278 target = 0.202466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.175562 restraints weight = 6633.587| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.86 r_work: 0.3901 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3782 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2523 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= 0.125 Angle : 0.549 10.360 7067 Z= 0.285 Chirality : 0.041 0.141 786 Planarity : 0.004 0.041 867 Dihedral : 5.792 56.957 723 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.77 % Allowed : 17.34 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.33), residues: 637 helix: 1.76 (0.28), residues: 336 sheet: -0.61 (0.70), residues: 58 loop : -0.40 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.021 0.002 PHE A 413 TRP 0.012 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5207) covalent geometry : angle 0.54921 ( 7051) SS BOND : bond 0.00141 ( 8) SS BOND : angle 0.57040 ( 16) hydrogen bonds : bond 0.03563 ( 287) hydrogen bonds : angle 4.72325 ( 855) *********************** 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 115 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 574 PHE cc_start: 0.7224 (t80) cc_final: 0.6966 (t80) REVERT: B 66 ASP cc_start: 0.7056 (m-30) cc_final: 0.6702 (m-30) outliers start: 15 outliers final: 12 residues processed: 110 average time/residue: 0.0739 time to fit residues: 10.6224 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 : 0.173 ------------------------------------------------------------------------------- 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 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 14 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.200719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.173659 restraints weight = 6578.798| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.86 r_work: 0.3888 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5215 Z= 0.141 Angle : 0.583 10.736 7067 Z= 0.303 Chirality : 0.042 0.200 786 Planarity : 0.004 0.041 867 Dihedral : 5.738 56.871 723 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.21 % Allowed : 18.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.33), residues: 637 helix: 1.74 (0.28), residues: 337 sheet: -0.67 (0.69), residues: 58 loop : -0.47 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.021 0.001 TYR A 590 PHE 0.020 0.002 PHE A 68 TRP 0.012 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 5207) covalent geometry : angle 0.58237 ( 7051) SS BOND : bond 0.00197 ( 8) SS BOND : angle 0.64095 ( 16) hydrogen bonds : bond 0.03686 ( 287) hydrogen bonds : angle 4.79064 ( 855) *********************** 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: 12 poor density : 100 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7353 (tm-30) REVERT: A 346 LEU cc_start: 0.8265 (tt) cc_final: 0.7994 (tt) REVERT: A 364 GLU cc_start: 0.7773 (tt0) cc_final: 0.7436 (tt0) REVERT: B 66 ASP cc_start: 0.7035 (m-30) cc_final: 0.6688 (m-30) outliers start: 12 outliers final: 12 residues processed: 108 average time/residue: 0.0633 time to fit residues: 9.1348 Evaluate side-chains 105 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 9 VAL 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 28 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.200431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.173551 restraints weight = 6519.827| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.83 r_work: 0.3884 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3768 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2809 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= 0.140 Angle : 0.583 10.481 7067 Z= 0.304 Chirality : 0.042 0.167 786 Planarity : 0.004 0.041 867 Dihedral : 5.719 56.848 723 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.32 % Allowed : 18.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.33), residues: 637 helix: 1.71 (0.28), residues: 337 sheet: -0.61 (0.69), residues: 58 loop : -0.48 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 103 TYR 0.021 0.001 TYR A 590 PHE 0.019 0.002 PHE A 413 TRP 0.014 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5207) covalent geometry : angle 0.58249 ( 7051) SS BOND : bond 0.00140 ( 8) SS BOND : angle 0.61168 ( 16) hydrogen bonds : bond 0.03776 ( 287) hydrogen bonds : angle 4.87147 ( 855) *********************** 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 114 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 185 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7301 (tm-30) REVERT: A 346 LEU cc_start: 0.8231 (tt) cc_final: 0.7974 (tt) REVERT: A 364 GLU cc_start: 0.7828 (tt0) cc_final: 0.7521 (tt0) REVERT: A 467 GLU cc_start: 0.6711 (mt-10) cc_final: 0.6276 (mp0) REVERT: B 66 ASP cc_start: 0.7053 (m-30) cc_final: 0.6701 (m-30) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.0674 time to fit residues: 9.8486 Evaluate side-chains 109 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.183 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 0.0060 chunk 63 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.3794 ------------------------------------------------------------------------------- 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 = 0.4284 r_free = 0.4284 target = 0.202964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.176184 restraints weight = 6468.307| |-----------------------------------------------------------------------------| r_work (start): 0.4021 rms_B_bonded: 1.83 r_work: 0.3918 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3797 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5215 Z= 0.115 Angle : 0.556 9.205 7067 Z= 0.291 Chirality : 0.041 0.176 786 Planarity : 0.004 0.041 867 Dihedral : 5.520 55.547 723 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.58 % Allowed : 18.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.34), residues: 637 helix: 1.86 (0.28), residues: 335 sheet: -0.43 (0.71), residues: 58 loop : -0.46 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 103 TYR 0.023 0.001 TYR A 590 PHE 0.023 0.001 PHE A 413 TRP 0.015 0.001 TRP A 171 HIS 0.006 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 5207) covalent geometry : angle 0.55546 ( 7051) SS BOND : bond 0.00134 ( 8) SS BOND : angle 0.59728 ( 16) hydrogen bonds : bond 0.03485 ( 287) hydrogen bonds : angle 4.65402 ( 855) *********************** 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 108 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.194 Fit side-chains REVERT: A 185 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 346 LEU cc_start: 0.8182 (tt) cc_final: 0.7934 (tt) REVERT: A 364 GLU cc_start: 0.7859 (tt0) cc_final: 0.7535 (tt0) REVERT: A 401 LYS cc_start: 0.8708 (mmtp) cc_final: 0.8423 (mmmt) REVERT: B 57 SER cc_start: 0.8429 (t) cc_final: 0.8173 (m) REVERT: B 66 ASP cc_start: 0.6988 (m-30) cc_final: 0.6631 (m-30) outliers start: 14 outliers final: 11 residues processed: 104 average time/residue: 0.0766 time to fit residues: 10.3130 Evaluate side-chains 102 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.127 ------------------------------------------------------------------------------- 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 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 26 CYS Chi-restraints excluded: chain B residue 56 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 49 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 0.0070 chunk 32 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.4273 r_free = 0.4273 target = 0.201825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174815 restraints weight = 6533.324| |-----------------------------------------------------------------------------| r_work (start): 0.4007 rms_B_bonded: 1.84 r_work: 0.3904 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3780 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 5215 Z= 0.130 Angle : 0.594 10.108 7067 Z= 0.310 Chirality : 0.042 0.256 786 Planarity : 0.004 0.041 867 Dihedral : 5.527 55.903 723 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.95 % Allowed : 18.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.33), residues: 637 helix: 1.81 (0.28), residues: 335 sheet: -0.35 (0.71), residues: 58 loop : -0.48 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 103 TYR 0.022 0.001 TYR A 590 PHE 0.022 0.002 PHE A 413 TRP 0.014 0.001 TRP A 171 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 5207) covalent geometry : angle 0.59410 ( 7051) SS BOND : bond 0.00159 ( 8) SS BOND : angle 0.61954 ( 16) hydrogen bonds : bond 0.03600 ( 287) hydrogen bonds : angle 4.74249 ( 855) ********************** 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: 16 poor density : 92 time to evaluate : 0.203 Fit side-chains REVERT: A 185 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 346 LEU cc_start: 0.8194 (tt) cc_final: 0.7942 (tt) REVERT: A 364 GLU cc_start: 0.7859 (tt0) cc_final: 0.7524 (tt0) REVERT: A 401 LYS cc_start: 0.8725 (mmtp) cc_final: 0.8419 (mmmt) REVERT: A 467 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6163 (mp0) REVERT: B 57 SER cc_start: 0.8477 (t) cc_final: 0.8201 (m) REVERT: B 66 ASP cc_start: 0.6966 (m-30) cc_final: 0.6622 (m-30) outliers start: 16 outliers final: 15 residues processed: 104 average time/residue: 0.0688 time to fit residues: 9.4814 Evaluate side-chains 107 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.193 ------------------------------------------------------------------------------- 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 560 VAL Chi-restraints excluded: chain A residue 637 LEU 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 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 14 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 16 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 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 516 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.202615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175619 restraints weight = 6597.220| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 1.86 r_work: 0.3912 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5215 Z= 0.122 Angle : 0.588 9.504 7067 Z= 0.304 Chirality : 0.043 0.322 786 Planarity : 0.004 0.041 867 Dihedral : 5.451 55.542 723 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.32 % Allowed : 18.08 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.33), residues: 637 helix: 1.71 (0.27), residues: 341 sheet: -0.28 (0.72), residues: 58 loop : -0.38 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 103 TYR 0.023 0.001 TYR A 590 PHE 0.022 0.002 PHE A 68 TRP 0.013 0.001 TRP A 171 HIS 0.007 0.001 HIS A 451 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 5207) covalent geometry : angle 0.58813 ( 7051) SS BOND : bond 0.00130 ( 8) SS BOND : angle 0.55878 ( 16) hydrogen bonds : bond 0.03523 ( 287) hydrogen bonds : angle 4.70906 ( 855) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1508.30 seconds wall clock time: 26 minutes 29.88 seconds (1589.88 seconds total)