Starting phenix.real_space_refine on Thu Jul 2 05:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jhm_61487/07_2026/9jhm_61487.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jhm_61487/07_2026/9jhm_61487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jhm_61487/07_2026/9jhm_61487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jhm_61487/07_2026/9jhm_61487.map" model { file = "/net/cci-nas-00/data/ceres_data/9jhm_61487/07_2026/9jhm_61487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jhm_61487/07_2026/9jhm_61487.cif" } 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 1 7.51 5 P 35 5.49 5 S 20 5.16 5 C 4244 2.51 5 N 1115 2.21 5 O 1340 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6755 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6036 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 359 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Chain: "E" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 359 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 1 Time building chain proxies: 1.46, per 1000 atoms: 0.22 Number of scatterers: 6755 At special positions: 0 Unit cell: (71.34, 83.64, 102.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 1 24.99 S 20 16.00 P 35 15.00 O 1340 8.00 N 1115 7.00 C 4244 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: 0.43 Conformation dependent library (CDL) restraints added in 333.9 milliseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 11 sheets defined 31.4% alpha, 17.6% beta 7 base pairs and 24 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 3.926A pdb=" N ASN A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 115 removed outlier: 3.781A pdb=" N TYR A 101 " --> pdb=" O ASN A 97 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LYS A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 233 through 241 removed outlier: 3.686A pdb=" N TYR A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 297 removed outlier: 3.574A pdb=" N SER A 293 " --> pdb=" O ASP A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 322 through 325 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 404 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 474 through 485 removed outlier: 3.642A pdb=" N PHE A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 508 through 522 Processing helix chain 'A' and resid 583 through 603 removed outlier: 4.296A pdb=" N LEU A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.646A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 711 removed outlier: 3.519A pdb=" N ALA A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 735 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 3.898A pdb=" N TYR A 175 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL A 172 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 removed outlier: 6.834A pdb=" N GLN A 28 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN A 83 " --> pdb=" O THR A 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 117 through 118 removed outlier: 3.534A pdb=" N TYR A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.563A pdb=" N LEU A 134 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 203 through 204 Processing sheet with id=AA6, first strand: chain 'A' and resid 215 through 223 removed outlier: 7.230A pdb=" N ASN A 261 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL A 219 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 259 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.625A pdb=" N SER A 663 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ILE A 690 " --> pdb=" O LYS A 641 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS A 641 " --> pdb=" O ILE A 690 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N LYS A 692 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU A 639 " --> pdb=" O LYS A 692 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 694 " --> pdb=" O ILE A 637 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 609 " --> pdb=" O LYS A 634 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N CYS A 539 " --> pdb=" O VAL A 610 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N HIS A 612 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N VAL A 541 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA A 614 " --> pdb=" O VAL A 541 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 543 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE A 540 " --> pdb=" O PHE A 561 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN A 569 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP A 745 " --> pdb=" O TYR A 570 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 359 removed outlier: 4.052A pdb=" N GLY A 357 " --> pdb=" O GLY A 354 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LEU A 352 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 529 " --> pdb=" O MET A 353 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 432 through 435 removed outlier: 6.483A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 461 " --> pdb=" O GLN A 490 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 407 through 408 Processing sheet with id=AB2, first strand: chain 'A' and resid 650 through 652 224 hydrogen bonds defined for protein. 627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 17 hydrogen bonds 34 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 24 stacking parallelities Total time for adding SS restraints: 1.28 Time building geometry restraints manager: 0.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1663 1.33 - 1.45: 1451 1.45 - 1.57: 3745 1.57 - 1.69: 69 1.69 - 1.81: 35 Bond restraints: 6963 Sorted by residual: bond pdb=" C3' DG C 8 " pdb=" O3' DG C 8 " ideal model delta sigma weight residual 1.435 1.381 0.054 1.30e-02 5.92e+03 1.74e+01 bond pdb=" C1' DC E 8 " pdb=" N1 DC E 8 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" C5' DA E 3 " pdb=" C4' DA E 3 " ideal model delta sigma weight residual 1.512 1.535 -0.023 7.00e-03 2.04e+04 1.05e+01 bond pdb=" C1' DT E 12 " pdb=" N1 DT E 12 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.01e+01 bond pdb=" C3' DT E 12 " pdb=" O3' DT E 12 " ideal model delta sigma weight residual 1.435 1.475 -0.040 1.30e-02 5.92e+03 9.64e+00 ... (remaining 6958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 9101 2.29 - 4.59: 376 4.59 - 6.88: 41 6.88 - 9.17: 16 9.17 - 11.46: 2 Bond angle restraints: 9536 Sorted by residual: angle pdb=" O4' DT C 9 " pdb=" C4' DT C 9 " pdb=" C3' DT C 9 " ideal model delta sigma weight residual 106.00 102.33 3.67 6.00e-01 2.78e+00 3.74e+01 angle pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta sigma weight residual 120.82 129.75 -8.93 1.50e+00 4.44e-01 3.54e+01 angle pdb=" C GLY A 264 " pdb=" N ASN A 265 " pdb=" CA ASN A 265 " ideal model delta sigma weight residual 121.54 132.52 -10.98 1.91e+00 2.74e-01 3.31e+01 angle pdb=" C GLU A 680 " pdb=" N ASN A 681 " pdb=" CA ASN A 681 " ideal model delta sigma weight residual 123.05 131.19 -8.14 1.57e+00 4.06e-01 2.69e+01 angle pdb=" O4' DG C 4 " pdb=" C1' DG C 4 " pdb=" N9 DG C 4 " ideal model delta sigma weight residual 108.00 111.53 -3.53 7.00e-01 2.04e+00 2.55e+01 ... (remaining 9531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 3846 24.08 - 48.15: 220 48.15 - 72.23: 59 72.23 - 96.31: 6 96.31 - 120.38: 1 Dihedral angle restraints: 4132 sinusoidal: 1945 harmonic: 2187 Sorted by residual: dihedral pdb=" CA GLU A 470 " pdb=" C GLU A 470 " pdb=" N ILE A 471 " pdb=" CA ILE A 471 " ideal model delta harmonic sigma weight residual -180.00 -123.31 -56.69 0 5.00e+00 4.00e-02 1.29e+02 dihedral pdb=" CA LYS A 63 " pdb=" C LYS A 63 " pdb=" N ASP A 64 " pdb=" CA ASP A 64 " ideal model delta harmonic sigma weight residual 180.00 -149.07 -30.93 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA THR A 507 " pdb=" C THR A 507 " pdb=" N ALA A 508 " pdb=" CA ALA A 508 " ideal model delta harmonic sigma weight residual 180.00 149.22 30.78 0 5.00e+00 4.00e-02 3.79e+01 ... (remaining 4129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 736 0.056 - 0.112: 221 0.112 - 0.168: 69 0.168 - 0.225: 10 0.225 - 0.281: 8 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CB ILE A 609 " pdb=" CA ILE A 609 " pdb=" CG1 ILE A 609 " pdb=" CG2 ILE A 609 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CB ILE A 712 " pdb=" CA ILE A 712 " pdb=" CG1 ILE A 712 " pdb=" CG2 ILE A 712 " both_signs ideal model delta sigma weight residual False 2.64 2.91 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CG LEU A 520 " pdb=" CB LEU A 520 " pdb=" CD1 LEU A 520 " pdb=" CD2 LEU A 520 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1041 not shown) Planarity restraints: 1090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 470 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C GLU A 470 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU A 470 " 0.020 2.00e-02 2.50e+03 pdb=" N ILE A 471 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 468 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.07e+00 pdb=" C ASP A 468 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP A 468 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A 469 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 623 " -0.017 2.00e-02 2.50e+03 1.35e-02 4.58e+00 pdb=" CG TRP A 623 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 623 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 623 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 623 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 623 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 623 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 623 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 623 " -0.006 2.00e-02 2.50e+03 ... (remaining 1087 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 24 2.43 - 3.05: 3767 3.05 - 3.66: 10732 3.66 - 4.28: 15928 4.28 - 4.90: 25357 Nonbonded interactions: 55808 Sorted by model distance: nonbonded pdb=" OP2 DT C 1 " pdb="MN MN C 801 " model vdw 1.811 3.060 nonbonded pdb=" OP1 DA C 3 " pdb="MN MN C 801 " model vdw 1.863 3.060 nonbonded pdb=" O LEU A 751 " pdb="MN MN C 801 " model vdw 1.906 3.060 nonbonded pdb=" OP1 DT C 1 " pdb="MN MN C 801 " model vdw 2.066 3.060 nonbonded pdb=" O ILE A 515 " pdb=" CG1 ILE A 519 " model vdw 2.099 3.440 ... (remaining 55803 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: 1.480 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.040 Find NCS groups from input model: 0.030 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 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 : 0.007 0.067 6963 Z= 0.394 Angle : 1.063 11.464 9536 Z= 0.666 Chirality : 0.064 0.281 1044 Planarity : 0.006 0.046 1090 Dihedral : 15.776 120.385 2738 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.38 % Favored : 94.48 % Rotamer: Outliers : 0.15 % Allowed : 4.19 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.83 (0.25), residues: 743 helix: -2.62 (0.26), residues: 197 sheet: -2.85 (0.36), residues: 147 loop : -2.34 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 158 TYR 0.026 0.003 TYR A 238 PHE 0.030 0.004 PHE A 154 TRP 0.034 0.004 TRP A 623 HIS 0.004 0.002 HIS A 713 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.39 ( 6963) covalent geometry : angle 1.06276 / 0.67 ( 9536) hydrogen bonds : bond 0.20549 / 12.78 ( 241) hydrogen bonds : angle 9.69942 / 6.55 ( 661) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.8179 (mmt) cc_final: 0.7571 (mmt) REVERT: A 294 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8808 (mmmt) REVERT: A 480 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8751 (pttp) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.0829 time to fit residues: 15.2224 Evaluate side-chains 77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 155 ASN A 243 GLN A 513 HIS ** A 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.121773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.097362 restraints weight = 20385.955| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 5.41 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 6963 Z= 0.186 Angle : 0.802 9.547 9536 Z= 0.436 Chirality : 0.051 0.265 1044 Planarity : 0.005 0.040 1090 Dihedral : 18.800 121.665 1199 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.54 % Allowed : 9.28 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.04 (0.27), residues: 743 helix: -1.55 (0.30), residues: 224 sheet: -2.36 (0.39), residues: 151 loop : -2.10 (0.28), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 618 TYR 0.040 0.002 TYR A 238 PHE 0.025 0.003 PHE A 591 TRP 0.045 0.005 TRP A 623 HIS 0.007 0.002 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.19 ( 6963) covalent geometry : angle 0.80209 / 0.44 ( 9536) hydrogen bonds : bond 0.05597 / 3.69 ( 241) hydrogen bonds : angle 7.22871 / 4.88 ( 661) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8680 (mtm) cc_final: 0.8286 (ptp) REVERT: A 98 MET cc_start: 0.7931 (mmt) cc_final: 0.7317 (mmt) REVERT: A 294 LYS cc_start: 0.9391 (mmmm) cc_final: 0.8916 (mmmt) REVERT: A 298 GLN cc_start: 0.8844 (mp10) cc_final: 0.8487 (mp10) REVERT: A 363 MET cc_start: 0.8992 (mmt) cc_final: 0.8592 (mmm) REVERT: A 480 LYS cc_start: 0.8981 (mtmt) cc_final: 0.8647 (pttm) REVERT: A 498 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8675 (mp0) REVERT: A 533 MET cc_start: 0.8281 (mmm) cc_final: 0.7616 (mmm) REVERT: A 595 LEU cc_start: 0.9376 (tp) cc_final: 0.9168 (pp) REVERT: A 646 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8464 (tm) outliers start: 17 outliers final: 6 residues processed: 103 average time/residue: 0.0665 time to fit residues: 9.6404 Evaluate side-chains 87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 155 ASN Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 55 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 0.0010 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 66 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 473 ASN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.121293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.096640 restraints weight = 20255.918| |-----------------------------------------------------------------------------| r_work (start): 0.3820 rms_B_bonded: 5.49 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6963 Z= 0.159 Angle : 0.733 10.455 9536 Z= 0.398 Chirality : 0.050 0.230 1044 Planarity : 0.004 0.031 1090 Dihedral : 18.585 120.137 1199 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.25 % Favored : 94.62 % Rotamer: Outliers : 2.25 % Allowed : 11.68 % Favored : 86.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.56 (0.27), residues: 743 helix: -1.29 (0.31), residues: 223 sheet: -2.28 (0.44), residues: 116 loop : -1.73 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 618 TYR 0.052 0.002 TYR A 238 PHE 0.018 0.002 PHE A 738 TRP 0.067 0.006 TRP A 623 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 ( 6963) covalent geometry : angle 0.73320 / 0.40 ( 9536) hydrogen bonds : bond 0.04837 / 3.19 ( 241) hydrogen bonds : angle 6.87916 / 4.68 ( 661) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8758 (mtm) cc_final: 0.8154 (ptp) REVERT: A 58 LYS cc_start: 0.9387 (mmtp) cc_final: 0.8847 (mmmm) REVERT: A 98 MET cc_start: 0.7877 (mmt) cc_final: 0.7302 (mmt) REVERT: A 197 GLU cc_start: 0.8573 (tp30) cc_final: 0.8366 (tp30) REVERT: A 294 LYS cc_start: 0.9397 (mmmm) cc_final: 0.9001 (mmmt) REVERT: A 298 GLN cc_start: 0.8863 (mp10) cc_final: 0.8470 (mp10) REVERT: A 337 VAL cc_start: 0.8536 (OUTLIER) cc_final: 0.8298 (t) REVERT: A 363 MET cc_start: 0.8943 (mmt) cc_final: 0.8545 (mmt) REVERT: A 480 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8681 (pttm) REVERT: A 533 MET cc_start: 0.8299 (mmm) cc_final: 0.7946 (mmm) REVERT: A 646 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8475 (tm) outliers start: 15 outliers final: 6 residues processed: 102 average time/residue: 0.0821 time to fit residues: 11.4736 Evaluate side-chains 95 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 0.2980 chunk 57 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 1 optimal weight: 0.0770 chunk 24 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 overall best weight: 2.2744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN A 288 ASN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.115262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.091079 restraints weight = 21478.079| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 5.36 r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6963 Z= 0.211 Angle : 0.718 9.107 9536 Z= 0.392 Chirality : 0.048 0.202 1044 Planarity : 0.004 0.045 1090 Dihedral : 18.491 119.625 1199 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.14 % Allowed : 11.53 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.28 (0.28), residues: 743 helix: -1.01 (0.32), residues: 228 sheet: -2.03 (0.44), residues: 128 loop : -1.58 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 618 TYR 0.032 0.002 TYR A 238 PHE 0.014 0.002 PHE A 591 TRP 0.076 0.007 TRP A 623 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 ( 6963) covalent geometry : angle 0.71765 / 0.39 ( 9536) hydrogen bonds : bond 0.04543 / 3.03 ( 241) hydrogen bonds : angle 6.55922 / 4.50 ( 661) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8959 (mtm) cc_final: 0.8403 (ptp) REVERT: A 55 ASN cc_start: 0.9532 (p0) cc_final: 0.8950 (p0) REVERT: A 98 MET cc_start: 0.7946 (mmt) cc_final: 0.7353 (mmt) REVERT: A 294 LYS cc_start: 0.9391 (mmmm) cc_final: 0.9076 (mmmt) REVERT: A 311 LEU cc_start: 0.8385 (mt) cc_final: 0.7737 (tp) REVERT: A 337 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8406 (t) REVERT: A 363 MET cc_start: 0.8910 (mmt) cc_final: 0.8227 (mmm) REVERT: A 533 MET cc_start: 0.8298 (mmm) cc_final: 0.7819 (mmm) REVERT: A 646 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8570 (tm) outliers start: 21 outliers final: 12 residues processed: 105 average time/residue: 0.0740 time to fit residues: 10.7411 Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 58 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 75 optimal weight: 20.0000 chunk 47 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** 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 = 0.4266 r_free = 0.4266 target = 0.121821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.096923 restraints weight = 21071.201| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 5.51 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6963 Z= 0.157 Angle : 0.721 10.977 9536 Z= 0.383 Chirality : 0.048 0.221 1044 Planarity : 0.004 0.037 1090 Dihedral : 18.404 119.250 1199 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.99 % Allowed : 12.72 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.23 (0.29), residues: 743 helix: -1.07 (0.32), residues: 230 sheet: -1.96 (0.45), residues: 128 loop : -1.49 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 56 TYR 0.027 0.002 TYR A 238 PHE 0.022 0.002 PHE A 61 TRP 0.064 0.006 TRP A 623 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 ( 6963) covalent geometry : angle 0.72097 / 0.38 ( 9536) hydrogen bonds : bond 0.04178 / 2.77 ( 241) hydrogen bonds : angle 6.45826 / 4.41 ( 661) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.8970 (mtm) cc_final: 0.8357 (ptp) REVERT: A 55 ASN cc_start: 0.9296 (p0) cc_final: 0.8904 (p0) REVERT: A 98 MET cc_start: 0.7932 (mmt) cc_final: 0.7375 (mmt) REVERT: A 294 LYS cc_start: 0.9369 (mmmm) cc_final: 0.8931 (mmmt) REVERT: A 295 GLU cc_start: 0.9331 (tp30) cc_final: 0.9123 (tp30) REVERT: A 363 MET cc_start: 0.8878 (mmt) cc_final: 0.8186 (mmm) REVERT: A 454 ASN cc_start: 0.8955 (t0) cc_final: 0.8753 (t0) REVERT: A 466 MET cc_start: 0.8010 (ptp) cc_final: 0.7567 (pmm) REVERT: A 480 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8748 (mtpp) REVERT: A 498 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8733 (mm-30) REVERT: A 567 LEU cc_start: 0.8896 (tt) cc_final: 0.8661 (tt) REVERT: A 646 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8595 (tm) outliers start: 20 outliers final: 11 residues processed: 109 average time/residue: 0.0788 time to fit residues: 12.0425 Evaluate side-chains 94 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 688 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 232 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** A 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.121533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.096891 restraints weight = 21241.356| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 5.50 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6963 Z= 0.153 Angle : 0.700 9.697 9536 Z= 0.375 Chirality : 0.048 0.223 1044 Planarity : 0.004 0.040 1090 Dihedral : 18.311 119.404 1199 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 3.29 % Allowed : 13.62 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.08 (0.29), residues: 743 helix: -0.96 (0.32), residues: 230 sheet: -1.94 (0.44), residues: 129 loop : -1.36 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 613 TYR 0.026 0.002 TYR A 49 PHE 0.021 0.002 PHE A 147 TRP 0.035 0.004 TRP A 528 HIS 0.006 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 ( 6963) covalent geometry : angle 0.70003 / 0.37 ( 9536) hydrogen bonds : bond 0.04000 / 2.65 ( 241) hydrogen bonds : angle 6.27300 / 4.29 ( 661) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8437 (tt0) cc_final: 0.7892 (tm-30) REVERT: A 24 MET cc_start: 0.9004 (mtm) cc_final: 0.8392 (ptp) REVERT: A 55 ASN cc_start: 0.9271 (p0) cc_final: 0.8413 (p0) REVERT: A 56 ARG cc_start: 0.8248 (mmp80) cc_final: 0.8012 (mmp80) REVERT: A 98 MET cc_start: 0.7981 (mmt) cc_final: 0.7418 (mmt) REVERT: A 294 LYS cc_start: 0.9383 (mmmm) cc_final: 0.8948 (mmmt) REVERT: A 363 MET cc_start: 0.8870 (mmt) cc_final: 0.8162 (mmm) REVERT: A 454 ASN cc_start: 0.8986 (t0) cc_final: 0.8773 (t0) REVERT: A 466 MET cc_start: 0.8142 (ptp) cc_final: 0.7691 (pmm) REVERT: A 480 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8742 (mtpp) REVERT: A 567 LEU cc_start: 0.8922 (tt) cc_final: 0.8702 (tt) REVERT: A 646 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8575 (tm) outliers start: 22 outliers final: 10 residues processed: 103 average time/residue: 0.0652 time to fit residues: 9.4335 Evaluate side-chains 89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 7.9990 chunk 7 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** 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 = 0.4256 r_free = 0.4256 target = 0.120775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.096072 restraints weight = 20672.193| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 5.42 r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6963 Z= 0.170 Angle : 0.700 7.578 9536 Z= 0.374 Chirality : 0.048 0.229 1044 Planarity : 0.004 0.042 1090 Dihedral : 18.269 119.308 1199 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.40 % Allowed : 15.12 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.98 (0.29), residues: 743 helix: -0.91 (0.32), residues: 230 sheet: -1.91 (0.44), residues: 129 loop : -1.25 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 721 TYR 0.021 0.002 TYR A 49 PHE 0.018 0.002 PHE A 432 TRP 0.036 0.004 TRP A 528 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 ( 6963) covalent geometry : angle 0.69988 / 0.37 ( 9536) hydrogen bonds : bond 0.04024 / 2.69 ( 241) hydrogen bonds : angle 6.22043 / 4.24 ( 661) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.9044 (mtm) cc_final: 0.8399 (ptp) REVERT: A 55 ASN cc_start: 0.9264 (p0) cc_final: 0.9013 (p0) REVERT: A 98 MET cc_start: 0.8022 (mmt) cc_final: 0.7460 (mmt) REVERT: A 294 LYS cc_start: 0.9355 (mmmm) cc_final: 0.8832 (mmmt) REVERT: A 298 GLN cc_start: 0.8973 (mp10) cc_final: 0.8539 (mp10) REVERT: A 311 LEU cc_start: 0.8300 (mt) cc_final: 0.8078 (tp) REVERT: A 363 MET cc_start: 0.8865 (mmt) cc_final: 0.8462 (mmt) REVERT: A 454 ASN cc_start: 0.9035 (t0) cc_final: 0.8828 (t0) REVERT: A 480 LYS cc_start: 0.8967 (mtmt) cc_final: 0.8743 (mtpp) REVERT: A 498 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8717 (mm-30) REVERT: A 533 MET cc_start: 0.8081 (mmm) cc_final: 0.7718 (mmm) REVERT: A 646 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8599 (tm) outliers start: 16 outliers final: 13 residues processed: 92 average time/residue: 0.0674 time to fit residues: 8.6789 Evaluate side-chains 89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 54 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 741 GLN ** 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 = 0.4100 r_free = 0.4100 target = 0.109993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.086574 restraints weight = 22366.275| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 5.37 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 6963 Z= 0.227 Angle : 0.730 7.891 9536 Z= 0.393 Chirality : 0.048 0.263 1044 Planarity : 0.004 0.054 1090 Dihedral : 18.319 120.404 1199 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 2.84 % Allowed : 15.57 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.92 (0.29), residues: 743 helix: -0.95 (0.31), residues: 233 sheet: -1.82 (0.45), residues: 130 loop : -1.18 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 721 TYR 0.024 0.002 TYR A 49 PHE 0.028 0.003 PHE A 147 TRP 0.031 0.004 TRP A 528 HIS 0.007 0.002 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 ( 6963) covalent geometry : angle 0.72951 / 0.39 ( 9536) hydrogen bonds : bond 0.04248 / 2.93 ( 241) hydrogen bonds : angle 6.29038 / 4.31 ( 661) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.9114 (mtm) cc_final: 0.8494 (ptp) REVERT: A 55 ASN cc_start: 0.9274 (p0) cc_final: 0.8998 (p0) REVERT: A 98 MET cc_start: 0.8147 (mmt) cc_final: 0.7576 (mmt) REVERT: A 169 MET cc_start: 0.9175 (mmm) cc_final: 0.8797 (ttm) REVERT: A 197 GLU cc_start: 0.8630 (tp30) cc_final: 0.8392 (tm-30) REVERT: A 283 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8556 (tm-30) REVERT: A 294 LYS cc_start: 0.9380 (mmmm) cc_final: 0.8970 (mmmt) REVERT: A 311 LEU cc_start: 0.8512 (mt) cc_final: 0.8281 (tp) REVERT: A 363 MET cc_start: 0.8805 (mmt) cc_final: 0.8378 (mmt) REVERT: A 466 MET cc_start: 0.8404 (ptp) cc_final: 0.7955 (pmm) REVERT: A 480 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8808 (mtpp) REVERT: A 498 GLU cc_start: 0.9090 (mt-10) cc_final: 0.8694 (mm-30) REVERT: A 567 LEU cc_start: 0.9030 (tt) cc_final: 0.8830 (tt) REVERT: A 600 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9216 (pt0) REVERT: A 646 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8713 (tm) REVERT: A 673 MET cc_start: 0.8166 (ttp) cc_final: 0.7950 (ttt) REVERT: A 734 LYS cc_start: 0.9381 (pttp) cc_final: 0.9023 (pttm) outliers start: 19 outliers final: 12 residues processed: 94 average time/residue: 0.0659 time to fit residues: 8.7299 Evaluate side-chains 85 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 7 optimal weight: 0.0980 chunk 44 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** 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 = 0.4167 r_free = 0.4167 target = 0.116565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.092037 restraints weight = 21463.046| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 5.44 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6963 Z= 0.160 Angle : 0.713 10.422 9536 Z= 0.381 Chirality : 0.048 0.238 1044 Planarity : 0.004 0.051 1090 Dihedral : 18.275 117.997 1199 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.40 % Allowed : 16.62 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.84 (0.30), residues: 743 helix: -0.96 (0.31), residues: 234 sheet: -1.77 (0.45), residues: 131 loop : -1.06 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.021 0.002 TYR A 49 PHE 0.026 0.002 PHE A 147 TRP 0.035 0.004 TRP A 528 HIS 0.005 0.001 HIS A 409 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 6963) covalent geometry : angle 0.71350 / 0.38 ( 9536) hydrogen bonds : bond 0.03961 / 2.71 ( 241) hydrogen bonds : angle 6.19618 / 4.23 ( 661) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8473 (tt0) cc_final: 0.7929 (tm-30) REVERT: A 24 MET cc_start: 0.9124 (mtm) cc_final: 0.8454 (ptp) REVERT: A 55 ASN cc_start: 0.9290 (p0) cc_final: 0.9047 (p0) REVERT: A 98 MET cc_start: 0.8110 (mmt) cc_final: 0.7547 (mmt) REVERT: A 169 MET cc_start: 0.9207 (mmm) cc_final: 0.8797 (ttm) REVERT: A 197 GLU cc_start: 0.8660 (tp30) cc_final: 0.8413 (tm-30) REVERT: A 283 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8552 (tm-30) REVERT: A 294 LYS cc_start: 0.9345 (mmmm) cc_final: 0.8824 (mmmt) REVERT: A 298 GLN cc_start: 0.9006 (mp10) cc_final: 0.8584 (mp10) REVERT: A 363 MET cc_start: 0.8848 (mmt) cc_final: 0.8409 (mmt) REVERT: A 480 LYS cc_start: 0.8969 (mtmt) cc_final: 0.8732 (mtpp) REVERT: A 533 MET cc_start: 0.8124 (mmm) cc_final: 0.7778 (mmm) REVERT: A 646 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8583 (tm) outliers start: 16 outliers final: 12 residues processed: 94 average time/residue: 0.0624 time to fit residues: 8.1768 Evaluate side-chains 91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 11 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.0270 chunk 68 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** 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 = 0.4123 r_free = 0.4123 target = 0.111321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.088781 restraints weight = 22053.333| |-----------------------------------------------------------------------------| r_work (start): 0.3808 rms_B_bonded: 5.28 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6963 Z= 0.165 Angle : 0.724 8.717 9536 Z= 0.383 Chirality : 0.048 0.243 1044 Planarity : 0.004 0.049 1090 Dihedral : 18.261 118.818 1199 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.40 % Allowed : 16.92 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.76 (0.30), residues: 743 helix: -0.97 (0.31), residues: 234 sheet: -1.71 (0.45), residues: 131 loop : -0.97 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 721 TYR 0.021 0.002 TYR A 49 PHE 0.024 0.002 PHE A 147 TRP 0.031 0.004 TRP A 528 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 ( 6963) covalent geometry : angle 0.72423 / 0.38 ( 9536) hydrogen bonds : bond 0.03949 / 2.70 ( 241) hydrogen bonds : angle 6.11788 / 4.18 ( 661) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8493 (tt0) cc_final: 0.7955 (tm-30) REVERT: A 24 MET cc_start: 0.9069 (mtm) cc_final: 0.8457 (ptp) REVERT: A 55 ASN cc_start: 0.9213 (p0) cc_final: 0.8967 (p0) REVERT: A 98 MET cc_start: 0.8176 (mmt) cc_final: 0.7578 (mmt) REVERT: A 169 MET cc_start: 0.9154 (mmm) cc_final: 0.8783 (ttm) REVERT: A 283 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8546 (tm-30) REVERT: A 294 LYS cc_start: 0.9379 (mmmm) cc_final: 0.8848 (mmmt) REVERT: A 298 GLN cc_start: 0.8971 (mp10) cc_final: 0.8583 (mp10) REVERT: A 363 MET cc_start: 0.8796 (mmt) cc_final: 0.8485 (mmt) REVERT: A 480 LYS cc_start: 0.9062 (mtmt) cc_final: 0.8805 (mtpp) REVERT: A 533 MET cc_start: 0.8130 (mmm) cc_final: 0.7762 (mmm) REVERT: A 646 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8664 (tm) REVERT: A 734 LYS cc_start: 0.9350 (pttp) cc_final: 0.8943 (pttp) outliers start: 16 outliers final: 13 residues processed: 87 average time/residue: 0.0758 time to fit residues: 8.9140 Evaluate side-chains 87 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 THR Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 516 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 30 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 54 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 66 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 741 GLN ** 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 = 0.4248 r_free = 0.4248 target = 0.121557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.096495 restraints weight = 20974.746| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 5.57 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6963 Z= 0.172 Angle : 0.743 14.060 9536 Z= 0.389 Chirality : 0.048 0.236 1044 Planarity : 0.004 0.048 1090 Dihedral : 18.267 118.428 1199 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.25 % Allowed : 17.37 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -1.69 (0.30), residues: 743 helix: -0.94 (0.31), residues: 233 sheet: -1.63 (0.46), residues: 130 loop : -0.92 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 721 TYR 0.022 0.001 TYR A 49 PHE 0.017 0.002 PHE A 147 TRP 0.032 0.004 TRP A 528 HIS 0.005 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 6963) covalent geometry : angle 0.74270 / 0.39 ( 9536) hydrogen bonds : bond 0.03848 / 2.62 ( 241) hydrogen bonds : angle 6.07167 / 4.15 ( 661) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1385.83 seconds wall clock time: 24 minutes 41.19 seconds (1481.19 seconds total)