Starting phenix.real_space_refine on Tue Aug 4 16:42:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vd0_64972/08_2026/9vd0_64972.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vd0_64972/08_2026/9vd0_64972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vd0_64972/08_2026/9vd0_64972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vd0_64972/08_2026/9vd0_64972.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vd0_64972/08_2026/9vd0_64972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vd0_64972/08_2026/9vd0_64972.map" } resolution = 4.42 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= 1.000 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 P 5 5.49 5 S 28 5.16 5 C 3122 2.51 5 N 835 2.21 5 O 908 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4898 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Classifications: {'RNA': 2} Modifications used: {'rna2p_pyr': 1} Link IDs: {'rna2p': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 4828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4828 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 32, 'TRANS': 570} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.38, per 1000 atoms: 0.28 Number of scatterers: 4898 At special positions: 0 Unit cell: (79.68, 79.68, 110.39, 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 28 16.00 P 5 15.00 O 908 8.00 N 835 7.00 C 3122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.48 Conformation dependent library (CDL) restraints added in 214.0 milliseconds 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1150 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 3 sheets defined 59.4% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 103 through 113 Processing helix chain 'A' and resid 116 through 134 Processing helix chain 'A' and resid 138 through 150 Processing helix chain 'A' and resid 154 through 157 Processing helix chain 'A' and resid 158 through 170 Processing helix chain 'A' and resid 171 through 183 removed outlier: 7.022A pdb=" N ASP A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ASP A 178 " --> pdb=" O ASP A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 192 through 198 removed outlier: 3.794A pdb=" N MET A 198 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.650A pdb=" N ALA A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 247 removed outlier: 3.591A pdb=" N ALA A 237 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 301 through 312 removed outlier: 4.074A pdb=" N TRP A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 360 through 364 Processing helix chain 'A' and resid 374 through 388 Processing helix chain 'A' and resid 400 through 412 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.699A pdb=" N MET A 429 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 Processing helix chain 'A' and resid 487 through 500 removed outlier: 4.027A pdb=" N SER A 492 " --> pdb=" O HIS A 488 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 493 " --> pdb=" O GLU A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 524 Processing helix chain 'A' and resid 528 through 539 Processing helix chain 'A' and resid 551 through 561 Processing helix chain 'A' and resid 567 through 577 Processing helix chain 'A' and resid 583 through 599 removed outlier: 3.738A pdb=" N CYS A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 Processing helix chain 'A' and resid 621 through 643 removed outlier: 3.586A pdb=" N TYR A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 672 removed outlier: 3.747A pdb=" N ASN A 672 " --> pdb=" O ASP A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 685 removed outlier: 3.568A pdb=" N LEU A 685 " --> pdb=" O GLU A 681 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 259 through 260 removed outlier: 6.203A pdb=" N ASP A 252 " --> pdb=" O SER A 273 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR A 275 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL A 254 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLY A 227 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N CYS A 274 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N TYR A 229 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL A 228 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU A 286 " --> pdb=" O GLU A 316 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N HIS A 318 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA A 288 " --> pdb=" O HIS A 318 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N CYS A 320 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 290 " --> pdb=" O CYS A 320 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LYS A 201 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N LEU A 319 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 203 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 202 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N ARG A 343 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE A 204 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.651A pdb=" N SER A 352 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N THR A 485 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ILE A 438 " --> pdb=" O THR A 484 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N CYS A 369 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 421 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 423 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA A 393 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 448 removed outlier: 3.533A pdb=" N LYS A 445 " --> pdb=" O GLU A 457 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 457 " --> pdb=" O LYS A 445 " (cutoff:3.500A) 233 hydrogen bonds defined for protein. 669 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: 0.87 Time building geometry restraints manager: 0.65 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: 1554 1.34 - 1.46: 645 1.46 - 1.57: 2764 1.57 - 1.69: 6 1.69 - 1.81: 44 Bond restraints: 5013 Sorted by residual: bond pdb=" C6 ANP A 801 " pdb=" N6 ANP A 801 " ideal model delta sigma weight residual 1.340 1.444 -0.104 2.00e-02 2.50e+03 2.68e+01 bond pdb=" C8 ANP A 801 " pdb=" N9 ANP A 801 " ideal model delta sigma weight residual 1.369 1.272 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C4' ANP A 801 " pdb=" O4' ANP A 801 " ideal model delta sigma weight residual 1.431 1.517 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" C4 ANP A 801 " pdb=" N9 ANP A 801 " ideal model delta sigma weight residual 1.363 1.283 0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C1' ANP A 801 " pdb=" O4' ANP A 801 " ideal model delta sigma weight residual 1.394 1.472 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 5008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 6637 2.15 - 4.30: 118 4.30 - 6.44: 25 6.44 - 8.59: 13 8.59 - 10.74: 7 Bond angle restraints: 6800 Sorted by residual: angle pdb=" C1' U C 2 " pdb=" N1 U C 2 " pdb=" C2 U C 2 " ideal model delta sigma weight residual 117.70 126.49 -8.79 1.20e+00 6.94e-01 5.36e+01 angle pdb=" N1 U C 2 " pdb=" C2 U C 2 " pdb=" O2 U C 2 " ideal model delta sigma weight residual 122.80 127.33 -4.53 7.00e-01 2.04e+00 4.19e+01 angle pdb=" O2 U C 2 " pdb=" C2 U C 2 " pdb=" N3 U C 2 " ideal model delta sigma weight residual 122.20 118.05 4.15 7.00e-01 2.04e+00 3.51e+01 angle pdb=" C1' U C 2 " pdb=" N1 U C 2 " pdb=" C6 U C 2 " ideal model delta sigma weight residual 121.20 114.41 6.79 1.40e+00 5.10e-01 2.35e+01 angle pdb=" C2' U C 2 " pdb=" C1' U C 2 " pdb=" N1 U C 2 " ideal model delta sigma weight residual 112.00 117.27 -5.27 1.10e+00 8.26e-01 2.30e+01 ... (remaining 6795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.78: 2980 32.78 - 65.56: 76 65.56 - 98.35: 8 98.35 - 131.13: 0 131.13 - 163.91: 1 Dihedral angle restraints: 3065 sinusoidal: 1293 harmonic: 1772 Sorted by residual: dihedral pdb=" C4' U C 2 " pdb=" C3' U C 2 " pdb=" C2' U C 2 " pdb=" C1' U C 2 " ideal model delta sinusoidal sigma weight residual 36.34 -35.67 72.02 1 3.10e+00 1.04e-01 6.91e+02 dihedral pdb=" C5' U C 2 " pdb=" C4' U C 2 " pdb=" C3' U C 2 " pdb=" O3' U C 2 " ideal model delta sinusoidal sigma weight residual 201.84 145.75 56.10 3 5.20e+00 3.70e-02 7.81e+01 dihedral pdb=" O4' U C 1 " pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sinusoidal sigma weight residual 232.00 68.09 163.91 1 1.70e+01 3.46e-03 6.51e+01 ... (remaining 3062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 633 0.057 - 0.113: 107 0.113 - 0.170: 14 0.170 - 0.227: 2 0.227 - 0.284: 2 Chirality restraints: 758 Sorted by residual: chirality pdb=" C3' U C 2 " pdb=" C4' U C 2 " pdb=" O3' U C 2 " pdb=" C2' U C 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.76 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" P U C 2 " pdb=" OP1 U C 2 " pdb=" OP2 U C 2 " pdb=" O5' U C 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2' ANP A 801 " pdb=" C1' ANP A 801 " pdb=" C3' ANP A 801 " pdb=" O2' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.72 -2.50 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 755 not shown) Planarity restraints: 864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP A 614 " -0.067 5.00e-02 4.00e+02 1.03e-01 1.68e+01 pdb=" N PRO A 615 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 615 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO A 615 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 577 " 0.028 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO A 578 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 578 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 578 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 564 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 565 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 565 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 565 " 0.022 5.00e-02 4.00e+02 ... (remaining 861 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 101 2.69 - 3.24: 4922 3.24 - 3.79: 7729 3.79 - 4.35: 9982 4.35 - 4.90: 15993 Nonbonded interactions: 38727 Sorted by model distance: nonbonded pdb=" OG SER A 226 " pdb=" OE1 GLU A 286 " model vdw 2.132 3.040 nonbonded pdb=" NH1 ARG A 383 " pdb=" OE1 GLU A 386 " model vdw 2.240 3.120 nonbonded pdb=" OG SER A 374 " pdb=" OD1 ASN A 376 " model vdw 2.249 3.040 nonbonded pdb=" O LEU A 332 " pdb=" OG1 THR A 335 " model vdw 2.267 3.040 nonbonded pdb=" O GLN A 667 " pdb=" ND1 HIS A 671 " model vdw 2.281 3.120 ... (remaining 38722 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 group one per residue 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: 0.910 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: 7.270 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 5013 Z= 0.233 Angle : 0.799 10.742 6800 Z= 0.421 Chirality : 0.045 0.284 758 Planarity : 0.005 0.103 864 Dihedral : 14.723 163.911 1915 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % 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 : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.36), residues: 601 helix: 1.33 (0.31), residues: 310 sheet: 0.45 (0.62), residues: 82 loop : 0.03 (0.45), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 473 TYR 0.011 0.001 TYR A 396 PHE 0.010 0.001 PHE A 100 TRP 0.012 0.001 TRP A 614 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.23 ( 5013) covalent geometry : angle 0.79869 / 0.42 ( 6800) hydrogen bonds : bond 0.16012 / 11.23 ( 233) hydrogen bonds : angle 5.73530 / 4.46 ( 669) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.5372 (ppp) cc_final: 0.2438 (ttp) REVERT: A 203 ILE cc_start: 0.7949 (mm) cc_final: 0.7632 (mm) REVERT: A 294 GLN cc_start: 0.9017 (pp30) cc_final: 0.8694 (pp30) REVERT: A 320 CYS cc_start: 0.7251 (m) cc_final: 0.6883 (m) REVERT: A 375 LYS cc_start: 0.8080 (mppt) cc_final: 0.7303 (mmtm) REVERT: A 416 ASP cc_start: 0.7567 (m-30) cc_final: 0.7226 (m-30) REVERT: A 614 TRP cc_start: 0.6351 (t-100) cc_final: 0.5857 (t-100) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0751 time to fit residues: 11.3005 Evaluate side-chains 94 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.0870 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 667 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.193418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.146367 restraints weight = 9696.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.150242 restraints weight = 6704.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.152547 restraints weight = 5237.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.154475 restraints weight = 4436.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.155911 restraints weight = 3936.280| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5013 Z= 0.120 Angle : 0.573 6.802 6800 Z= 0.297 Chirality : 0.041 0.153 758 Planarity : 0.005 0.071 864 Dihedral : 10.938 176.490 711 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.35), residues: 601 helix: 1.49 (0.30), residues: 316 sheet: 0.36 (0.62), residues: 82 loop : 0.10 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 569 TYR 0.013 0.002 TYR A 396 PHE 0.019 0.001 PHE A 593 TRP 0.008 0.001 TRP A 614 HIS 0.007 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 5013) covalent geometry : angle 0.57313 / 0.30 ( 6800) hydrogen bonds : bond 0.04236 / 3.03 ( 233) hydrogen bonds : angle 4.32929 / 3.27 ( 669) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7785 (mm) cc_final: 0.7477 (mm) REVERT: A 294 GLN cc_start: 0.8812 (pp30) cc_final: 0.8540 (pp30) REVERT: A 320 CYS cc_start: 0.7058 (m) cc_final: 0.6700 (m) REVERT: A 358 LEU cc_start: 0.8560 (tp) cc_final: 0.8309 (tp) REVERT: A 375 LYS cc_start: 0.8095 (mppt) cc_final: 0.7467 (mmtm) REVERT: A 416 ASP cc_start: 0.7524 (m-30) cc_final: 0.7162 (m-30) REVERT: A 437 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7428 (ttp80) REVERT: A 626 MET cc_start: 0.9040 (mmp) cc_final: 0.8730 (mmp) REVERT: A 627 ASP cc_start: 0.8074 (m-30) cc_final: 0.7840 (m-30) REVERT: A 648 MET cc_start: 0.8965 (mmp) cc_final: 0.8733 (mmp) outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.0783 time to fit residues: 11.9793 Evaluate side-chains 91 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.191715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.144308 restraints weight = 9893.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147994 restraints weight = 6925.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150618 restraints weight = 5423.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.152462 restraints weight = 4571.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.153871 restraints weight = 4048.409| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5013 Z= 0.138 Angle : 0.578 6.001 6800 Z= 0.299 Chirality : 0.042 0.156 758 Planarity : 0.006 0.069 864 Dihedral : 10.936 179.362 711 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.35), residues: 601 helix: 1.51 (0.30), residues: 316 sheet: 0.28 (0.61), residues: 82 loop : 0.02 (0.45), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 569 TYR 0.020 0.002 TYR A 229 PHE 0.013 0.001 PHE A 593 TRP 0.009 0.001 TRP A 614 HIS 0.005 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 5013) covalent geometry : angle 0.57815 / 0.30 ( 6800) hydrogen bonds : bond 0.03786 / 2.65 ( 233) hydrogen bonds : angle 4.16948 / 3.09 ( 669) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7791 (mm) cc_final: 0.7442 (mm) REVERT: A 243 LYS cc_start: 0.7996 (mttt) cc_final: 0.7507 (mmtm) REVERT: A 294 GLN cc_start: 0.8831 (pp30) cc_final: 0.8531 (pp30) REVERT: A 320 CYS cc_start: 0.7335 (m) cc_final: 0.7075 (m) REVERT: A 358 LEU cc_start: 0.8556 (tp) cc_final: 0.8346 (tp) REVERT: A 379 TYR cc_start: 0.8356 (m-80) cc_final: 0.7902 (m-80) REVERT: A 416 ASP cc_start: 0.7534 (m-30) cc_final: 0.7197 (m-30) REVERT: A 626 MET cc_start: 0.8826 (mmp) cc_final: 0.8314 (mmm) REVERT: A 648 MET cc_start: 0.8890 (mmp) cc_final: 0.8675 (mmp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0744 time to fit residues: 11.3624 Evaluate side-chains 89 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 38 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.194009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145097 restraints weight = 9801.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.149184 restraints weight = 6625.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.152129 restraints weight = 5064.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.153785 restraints weight = 4210.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.155363 restraints weight = 3726.699| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5013 Z= 0.119 Angle : 0.552 6.048 6800 Z= 0.287 Chirality : 0.041 0.159 758 Planarity : 0.005 0.057 864 Dihedral : 10.793 179.688 711 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.35), residues: 601 helix: 1.51 (0.30), residues: 316 sheet: 0.29 (0.67), residues: 73 loop : -0.09 (0.43), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 569 TYR 0.019 0.002 TYR A 379 PHE 0.013 0.001 PHE A 593 TRP 0.008 0.001 TRP A 614 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5013) covalent geometry : angle 0.55222 / 0.29 ( 6800) hydrogen bonds : bond 0.03510 / 2.44 ( 233) hydrogen bonds : angle 4.11783 / 3.05 ( 669) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7709 (mm) cc_final: 0.7457 (mm) REVERT: A 243 LYS cc_start: 0.7922 (mttt) cc_final: 0.7411 (mmtm) REVERT: A 294 GLN cc_start: 0.8805 (pp30) cc_final: 0.8496 (pp30) REVERT: A 320 CYS cc_start: 0.7414 (m) cc_final: 0.7091 (m) REVERT: A 358 LEU cc_start: 0.8561 (tp) cc_final: 0.8293 (tp) REVERT: A 375 LYS cc_start: 0.7844 (mppt) cc_final: 0.7629 (mmtm) REVERT: A 379 TYR cc_start: 0.8408 (m-80) cc_final: 0.8048 (m-80) REVERT: A 416 ASP cc_start: 0.7540 (m-30) cc_final: 0.7043 (m-30) REVERT: A 437 ARG cc_start: 0.8286 (ttp80) cc_final: 0.7987 (ttp80) REVERT: A 648 MET cc_start: 0.8943 (mmp) cc_final: 0.8726 (mmp) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.0755 time to fit residues: 11.3566 Evaluate side-chains 93 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 0.0670 chunk 47 optimal weight: 0.9980 overall best weight: 1.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.189898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141851 restraints weight = 9913.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145592 restraints weight = 6653.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.148355 restraints weight = 5122.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.150214 restraints weight = 4256.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.151338 restraints weight = 3739.723| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5013 Z= 0.149 Angle : 0.605 6.206 6800 Z= 0.311 Chirality : 0.042 0.168 758 Planarity : 0.005 0.045 864 Dihedral : 10.698 179.845 711 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.19 % Allowed : 2.25 % Favored : 97.56 % 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 are not related in a simple way. whole: 1.06 (0.35), residues: 601 helix: 1.44 (0.30), residues: 317 sheet: 0.10 (0.66), residues: 73 loop : -0.08 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 569 TYR 0.023 0.002 TYR A 229 PHE 0.014 0.002 PHE A 593 TRP 0.010 0.002 TRP A 303 HIS 0.004 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 ( 5013) covalent geometry : angle 0.60492 / 0.31 ( 6800) hydrogen bonds : bond 0.03600 / 2.48 ( 233) hydrogen bonds : angle 4.18857 / 3.09 ( 669) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7915 (mttt) cc_final: 0.7386 (mmtm) REVERT: A 294 GLN cc_start: 0.8865 (pp30) cc_final: 0.8428 (pp30) REVERT: A 320 CYS cc_start: 0.7658 (m) cc_final: 0.7372 (m) REVERT: A 352 SER cc_start: 0.7585 (t) cc_final: 0.7238 (m) REVERT: A 358 LEU cc_start: 0.8568 (tp) cc_final: 0.8263 (tp) REVERT: A 375 LYS cc_start: 0.7840 (mppt) cc_final: 0.7584 (mmtm) REVERT: A 379 TYR cc_start: 0.8549 (m-80) cc_final: 0.8205 (m-80) REVERT: A 416 ASP cc_start: 0.7433 (m-30) cc_final: 0.6939 (m-30) REVERT: A 437 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8041 (ttp80) REVERT: A 626 MET cc_start: 0.9169 (mmp) cc_final: 0.8697 (mmp) REVERT: A 648 MET cc_start: 0.8911 (mmp) cc_final: 0.8677 (mmp) outliers start: 1 outliers final: 0 residues processed: 113 average time/residue: 0.0605 time to fit residues: 8.9187 Evaluate side-chains 87 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.192146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145539 restraints weight = 9980.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.149307 restraints weight = 6791.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.151983 restraints weight = 5244.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.153573 restraints weight = 4375.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.154964 restraints weight = 3883.353| |-----------------------------------------------------------------------------| r_work (final): 0.3971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5013 Z= 0.113 Angle : 0.569 6.447 6800 Z= 0.296 Chirality : 0.041 0.182 758 Planarity : 0.004 0.045 864 Dihedral : 10.524 179.264 711 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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 are not related in a simple way. whole: 1.06 (0.35), residues: 601 helix: 1.39 (0.29), residues: 317 sheet: 0.21 (0.67), residues: 73 loop : -0.03 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 644 TYR 0.022 0.002 TYR A 396 PHE 0.020 0.001 PHE A 127 TRP 0.008 0.001 TRP A 614 HIS 0.003 0.000 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 5013) covalent geometry : angle 0.56890 / 0.30 ( 6800) hydrogen bonds : bond 0.03485 / 2.44 ( 233) hydrogen bonds : angle 4.13278 / 3.08 ( 669) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 GLN cc_start: 0.8840 (pp30) cc_final: 0.8556 (pp30) REVERT: A 322 GLU cc_start: 0.8361 (pt0) cc_final: 0.8106 (pt0) REVERT: A 352 SER cc_start: 0.7519 (t) cc_final: 0.7181 (m) REVERT: A 358 LEU cc_start: 0.8534 (tp) cc_final: 0.8291 (tp) REVERT: A 375 LYS cc_start: 0.7807 (mppt) cc_final: 0.7349 (mmtm) REVERT: A 379 TYR cc_start: 0.8466 (m-80) cc_final: 0.8127 (m-80) REVERT: A 416 ASP cc_start: 0.7327 (m-30) cc_final: 0.6871 (m-30) REVERT: A 648 MET cc_start: 0.8912 (mmp) cc_final: 0.8584 (mmp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.0590 time to fit residues: 8.7528 Evaluate side-chains 91 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 37 optimal weight: 0.0870 chunk 13 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.0980 chunk 42 optimal weight: 0.2980 chunk 27 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.2958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.195254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147227 restraints weight = 9760.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.151083 restraints weight = 6689.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153962 restraints weight = 5135.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.155982 restraints weight = 4252.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.157039 restraints weight = 3704.053| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5013 Z= 0.109 Angle : 0.572 6.075 6800 Z= 0.295 Chirality : 0.041 0.183 758 Planarity : 0.005 0.058 864 Dihedral : 10.373 178.595 711 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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 are not related in a simple way. whole: 1.18 (0.35), residues: 601 helix: 1.46 (0.29), residues: 317 sheet: 0.49 (0.67), residues: 73 loop : -0.02 (0.43), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 437 TYR 0.021 0.002 TYR A 396 PHE 0.018 0.001 PHE A 127 TRP 0.005 0.001 TRP A 614 HIS 0.002 0.000 HIS A 671 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 5013) covalent geometry : angle 0.57158 / 0.30 ( 6800) hydrogen bonds : bond 0.03263 / 2.32 ( 233) hydrogen bonds : angle 4.08461 / 3.09 ( 669) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7583 (mm) cc_final: 0.7328 (mm) REVERT: A 278 MET cc_start: 0.8390 (mtp) cc_final: 0.7809 (mtp) REVERT: A 294 GLN cc_start: 0.8789 (pp30) cc_final: 0.8573 (pp30) REVERT: A 322 GLU cc_start: 0.8403 (pt0) cc_final: 0.8179 (pt0) REVERT: A 352 SER cc_start: 0.7377 (t) cc_final: 0.7070 (m) REVERT: A 358 LEU cc_start: 0.8533 (tp) cc_final: 0.8237 (tp) REVERT: A 375 LYS cc_start: 0.7792 (mppt) cc_final: 0.7352 (mmtm) REVERT: A 379 TYR cc_start: 0.8443 (m-80) cc_final: 0.8086 (m-80) REVERT: A 404 LYS cc_start: 0.7757 (mttt) cc_final: 0.7506 (ttpt) REVERT: A 416 ASP cc_start: 0.7224 (m-30) cc_final: 0.6706 (m-30) REVERT: A 437 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7690 (ttp80) REVERT: A 648 MET cc_start: 0.8920 (mmp) cc_final: 0.8531 (mmp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0495 time to fit residues: 7.4299 Evaluate side-chains 91 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 5 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.193382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.146058 restraints weight = 9797.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.150049 restraints weight = 6625.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.152631 restraints weight = 5089.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.153688 restraints weight = 4252.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155493 restraints weight = 3854.545| |-----------------------------------------------------------------------------| r_work (final): 0.3975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 5013 Z= 0.111 Angle : 0.572 7.127 6800 Z= 0.294 Chirality : 0.041 0.187 758 Planarity : 0.005 0.046 864 Dihedral : 10.238 178.812 711 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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 are not related in a simple way. whole: 1.21 (0.35), residues: 601 helix: 1.51 (0.29), residues: 317 sheet: 0.66 (0.72), residues: 63 loop : -0.10 (0.43), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 599 TYR 0.020 0.002 TYR A 396 PHE 0.017 0.001 PHE A 127 TRP 0.007 0.001 TRP A 614 HIS 0.003 0.000 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 5013) covalent geometry : angle 0.57202 / 0.29 ( 6800) hydrogen bonds : bond 0.03307 / 2.34 ( 233) hydrogen bonds : angle 4.11059 / 3.12 ( 669) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.7617 (mm) cc_final: 0.7347 (mm) REVERT: A 294 GLN cc_start: 0.8817 (pp30) cc_final: 0.8587 (pp30) REVERT: A 322 GLU cc_start: 0.8476 (pt0) cc_final: 0.8269 (pt0) REVERT: A 352 SER cc_start: 0.7409 (t) cc_final: 0.7108 (m) REVERT: A 358 LEU cc_start: 0.8494 (tp) cc_final: 0.8199 (tp) REVERT: A 375 LYS cc_start: 0.7800 (mppt) cc_final: 0.7127 (mptt) REVERT: A 379 TYR cc_start: 0.8445 (m-80) cc_final: 0.8076 (m-80) REVERT: A 416 ASP cc_start: 0.7134 (m-30) cc_final: 0.6632 (m-30) REVERT: A 437 ARG cc_start: 0.8113 (ttp80) cc_final: 0.7831 (ttp80) REVERT: A 626 MET cc_start: 0.9077 (mmp) cc_final: 0.8854 (mmm) REVERT: A 648 MET cc_start: 0.8843 (mmp) cc_final: 0.8481 (mmp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.0493 time to fit residues: 7.3513 Evaluate side-chains 90 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 26 optimal weight: 0.0970 chunk 56 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.192111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.144836 restraints weight = 9790.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.148659 restraints weight = 6726.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.151271 restraints weight = 5211.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.152712 restraints weight = 4372.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.154278 restraints weight = 3892.533| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5013 Z= 0.130 Angle : 0.598 6.949 6800 Z= 0.309 Chirality : 0.042 0.195 758 Planarity : 0.005 0.049 864 Dihedral : 10.229 179.167 711 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % 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 are not related in a simple way. whole: 1.05 (0.35), residues: 601 helix: 1.42 (0.29), residues: 319 sheet: 0.59 (0.71), residues: 63 loop : -0.26 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 599 TYR 0.019 0.002 TYR A 396 PHE 0.017 0.001 PHE A 127 TRP 0.009 0.001 TRP A 614 HIS 0.004 0.001 HIS A 271 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 5013) covalent geometry : angle 0.59781 / 0.31 ( 6800) hydrogen bonds : bond 0.03427 / 2.41 ( 233) hydrogen bonds : angle 4.26079 / 3.22 ( 669) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 CYS cc_start: 0.8355 (p) cc_final: 0.7999 (p) REVERT: A 294 GLN cc_start: 0.8811 (pp30) cc_final: 0.8503 (pp30) REVERT: A 352 SER cc_start: 0.7281 (t) cc_final: 0.6989 (m) REVERT: A 358 LEU cc_start: 0.8452 (tp) cc_final: 0.8131 (tp) REVERT: A 375 LYS cc_start: 0.7801 (mppt) cc_final: 0.7127 (mptt) REVERT: A 379 TYR cc_start: 0.8455 (m-10) cc_final: 0.8047 (m-80) REVERT: A 404 LYS cc_start: 0.7862 (mttt) cc_final: 0.7576 (ttpt) REVERT: A 416 ASP cc_start: 0.7085 (m-30) cc_final: 0.6618 (m-30) REVERT: A 437 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7866 (ttp80) REVERT: A 626 MET cc_start: 0.9058 (mmp) cc_final: 0.8787 (mmm) REVERT: A 629 GLU cc_start: 0.8852 (mp0) cc_final: 0.8641 (mp0) REVERT: A 648 MET cc_start: 0.8841 (mmp) cc_final: 0.8481 (mmp) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.0513 time to fit residues: 7.7574 Evaluate side-chains 96 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 42 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 23 optimal weight: 0.2980 chunk 12 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.190106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.141689 restraints weight = 9780.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.145678 restraints weight = 6575.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.148343 restraints weight = 5046.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.150177 restraints weight = 4210.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.151540 restraints weight = 3706.803| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5013 Z= 0.141 Angle : 0.616 6.903 6800 Z= 0.316 Chirality : 0.043 0.203 758 Planarity : 0.005 0.048 864 Dihedral : 10.193 179.631 711 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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 are not related in a simple way. whole: 0.98 (0.35), residues: 601 helix: 1.40 (0.29), residues: 319 sheet: 0.36 (0.70), residues: 63 loop : -0.26 (0.42), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 599 TYR 0.021 0.002 TYR A 229 PHE 0.030 0.002 PHE A 593 TRP 0.011 0.002 TRP A 614 HIS 0.004 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 ( 5013) covalent geometry : angle 0.61579 / 0.32 ( 6800) hydrogen bonds : bond 0.03517 / 2.48 ( 233) hydrogen bonds : angle 4.33607 / 3.24 ( 669) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1202 Ramachandran restraints generated. 601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 CYS cc_start: 0.8386 (p) cc_final: 0.7986 (p) REVERT: A 294 GLN cc_start: 0.8854 (pp30) cc_final: 0.8528 (pp30) REVERT: A 352 SER cc_start: 0.7385 (t) cc_final: 0.7068 (m) REVERT: A 375 LYS cc_start: 0.7802 (mppt) cc_final: 0.7114 (mptt) REVERT: A 379 TYR cc_start: 0.8469 (m-10) cc_final: 0.8042 (m-80) REVERT: A 416 ASP cc_start: 0.7081 (m-30) cc_final: 0.6617 (m-30) REVERT: A 437 ARG cc_start: 0.8396 (ttp80) cc_final: 0.8149 (ttp80) REVERT: A 474 PHE cc_start: 0.7707 (t80) cc_final: 0.7397 (t80) REVERT: A 539 PHE cc_start: 0.8148 (m-80) cc_final: 0.7914 (m-10) REVERT: A 593 PHE cc_start: 0.8037 (m-80) cc_final: 0.7833 (m-80) REVERT: A 626 MET cc_start: 0.8998 (mmp) cc_final: 0.8562 (mmm) REVERT: A 629 GLU cc_start: 0.8922 (mp0) cc_final: 0.8576 (mp0) REVERT: A 648 MET cc_start: 0.8878 (mmp) cc_final: 0.8455 (mmp) outliers start: 0 outliers final: 0 residues processed: 115 average time/residue: 0.0602 time to fit residues: 9.2057 Evaluate side-chains 96 residues out of total 533 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 11 optimal weight: 0.4980 chunk 42 optimal weight: 0.0050 chunk 54 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.192978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.145110 restraints weight = 9807.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.149078 restraints weight = 6653.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.151801 restraints weight = 5114.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153392 restraints weight = 4266.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.154818 restraints weight = 3793.126| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5013 Z= 0.113 Angle : 0.595 7.260 6800 Z= 0.309 Chirality : 0.042 0.204 758 Planarity : 0.005 0.085 864 Dihedral : 10.045 179.029 711 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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 are not related in a simple way. whole: 1.03 (0.35), residues: 601 helix: 1.44 (0.29), residues: 318 sheet: 0.34 (0.65), residues: 69 loop : -0.25 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 437 TYR 0.019 0.002 TYR A 396 PHE 0.039 0.002 PHE A 593 TRP 0.007 0.001 TRP A 614 HIS 0.003 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 ( 5013) covalent geometry : angle 0.59531 / 0.31 ( 6800) hydrogen bonds : bond 0.03304 / 2.33 ( 233) hydrogen bonds : angle 4.23416 / 3.19 ( 669) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1021.46 seconds wall clock time: 18 minutes 19.11 seconds (1099.11 seconds total)