Starting phenix.real_space_refine on Thu Jul 2 07:27:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9yxm_73611/07_2026/9yxm_73611_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9yxm_73611/07_2026/9yxm_73611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9yxm_73611/07_2026/9yxm_73611_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9yxm_73611/07_2026/9yxm_73611_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9yxm_73611/07_2026/9yxm_73611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9yxm_73611/07_2026/9yxm_73611.map" } resolution = 4.62 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= 0.010 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 62 5.49 5 S 32 5.16 5 C 4473 2.51 5 N 1287 2.21 5 O 1475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 7329 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 772, 6055 Classifications: {'peptide': 772} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 32, 'TRANS': 739} Chain breaks: 5 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 797 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "C" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 477 Classifications: {'DNA': 22, 'RNA': 1} Modifications used: {'rna3p_pur': 1} Link IDs: {'rna3p': 22} Time building chain proxies: 1.79, per 1000 atoms: 0.24 Number of scatterers: 7329 At special positions: 0 Unit cell: (73.04, 89.64, 144.42, 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 32 16.00 P 62 15.00 O 1475 8.00 N 1287 7.00 C 4473 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: 0.69 Conformation dependent library (CDL) restraints added in 431.8 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1446 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 60.2% alpha, 2.3% beta 14 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 Proline residue: A 20 - end of helix Processing helix chain 'A' and resid 29 through 45 removed outlier: 3.590A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 54 removed outlier: 4.457A pdb=" N ARG A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N MET A 54 " --> pdb=" O PHE A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 105 through 109 removed outlier: 3.746A pdb=" N GLU A 108 " --> pdb=" O PHE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 125 Processing helix chain 'A' and resid 133 through 151 Processing helix chain 'A' and resid 151 through 165 removed outlier: 3.502A pdb=" N HIS A 161 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 165 " --> pdb=" O HIS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 196 removed outlier: 3.676A pdb=" N LEU A 195 " --> pdb=" O SER A 192 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 196 " --> pdb=" O LYS A 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 192 through 196' Processing helix chain 'A' and resid 205 through 224 removed outlier: 3.938A pdb=" N SER A 209 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG A 215 " --> pdb=" O HIS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.596A pdb=" N GLU A 309 " --> pdb=" O MET A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 325 removed outlier: 3.560A pdb=" N ASN A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 Processing helix chain 'A' and resid 382 through 408 removed outlier: 3.790A pdb=" N GLU A 403 " --> pdb=" O GLU A 399 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 443 removed outlier: 3.598A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 468 Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 485 through 495 Processing helix chain 'A' and resid 501 through 505 removed outlier: 4.206A pdb=" N GLN A 505 " --> pdb=" O TRP A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 569 through 588 Processing helix chain 'A' and resid 612 through 624 Processing helix chain 'A' and resid 628 through 638 removed outlier: 4.271A pdb=" N ARG A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER A 633 " --> pdb=" O VAL A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 654 Processing helix chain 'A' and resid 654 through 662 removed outlier: 3.508A pdb=" N ALA A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 667 Processing helix chain 'A' and resid 669 through 688 removed outlier: 3.574A pdb=" N ALA A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 686 " --> pdb=" O TRP A 682 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 687 " --> pdb=" O GLU A 683 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 688 " --> pdb=" O SER A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 708 Processing helix chain 'A' and resid 750 through 754 Processing helix chain 'A' and resid 771 through 801 removed outlier: 5.590A pdb=" N ALA A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Proline residue: A 780 - end of helix Processing helix chain 'A' and resid 820 through 836 Processing helix chain 'A' and resid 840 through 853 removed outlier: 3.996A pdb=" N GLN A 852 " --> pdb=" O GLN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 860 removed outlier: 3.620A pdb=" N LEU A 858 " --> pdb=" O HIS A 854 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASP A 859 " --> pdb=" O GLU A 855 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LYS A 860 " --> pdb=" O SER A 856 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 854 through 860' Processing helix chain 'A' and resid 871 through 876 Processing sheet with id=AA1, first strand: chain 'A' and resid 227 through 230 removed outlier: 3.722A pdb=" N GLU A 245 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N HIS A 230 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A 243 " --> pdb=" O HIS A 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 330 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA4, first strand: chain 'A' and resid 450 through 451 removed outlier: 3.586A pdb=" N LYS A 450 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 726 through 727 removed outlier: 3.949A pdb=" N TRP A 727 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL A 735 " --> pdb=" O TRP A 727 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 744 through 746 300 hydrogen bonds defined for protein. 867 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 1.48 Time building geometry restraints manager: 0.93 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: 1910 1.34 - 1.46: 1726 1.46 - 1.58: 3806 1.58 - 1.70: 122 1.70 - 1.82: 54 Bond restraints: 7618 Sorted by residual: bond pdb=" C3' DT C 26 " pdb=" C2' DT C 26 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.29e+01 bond pdb=" C3' DC B 18 " pdb=" C2' DC B 18 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" N ASP A 770 " pdb=" CA ASP A 770 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" C3' DG B 22 " pdb=" C2' DG B 22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC B 36 " pdb=" C2' DC B 36 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 ... (remaining 7613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.67: 10157 2.67 - 5.34: 346 5.34 - 8.00: 52 8.00 - 10.67: 14 10.67 - 13.34: 4 Bond angle restraints: 10573 Sorted by residual: angle pdb=" O4' DA B 29 " pdb=" C4' DA B 29 " pdb=" C3' DA B 29 " ideal model delta sigma weight residual 106.00 102.57 3.43 6.00e-01 2.78e+00 3.26e+01 angle pdb=" CA GLU A 643 " pdb=" CB GLU A 643 " pdb=" CG GLU A 643 " ideal model delta sigma weight residual 114.10 123.67 -9.57 2.00e+00 2.50e-01 2.29e+01 angle pdb=" CA LYS A 614 " pdb=" CB LYS A 614 " pdb=" CG LYS A 614 " ideal model delta sigma weight residual 114.10 123.60 -9.50 2.00e+00 2.50e-01 2.25e+01 angle pdb=" CA LYS A 663 " pdb=" CB LYS A 663 " pdb=" CG LYS A 663 " ideal model delta sigma weight residual 114.10 123.14 -9.04 2.00e+00 2.50e-01 2.04e+01 angle pdb=" N3 DT C 11 " pdb=" C4 DT C 11 " pdb=" O4 DT C 11 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.00e+01 ... (remaining 10568 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 4087 35.79 - 71.57: 303 71.57 - 107.36: 22 107.36 - 143.14: 2 143.14 - 178.93: 2 Dihedral angle restraints: 4416 sinusoidal: 2182 harmonic: 2234 Sorted by residual: dihedral pdb=" CA ASP A 712 " pdb=" C ASP A 712 " pdb=" N LYS A 713 " pdb=" CA LYS A 713 " ideal model delta harmonic sigma weight residual -180.00 -152.09 -27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA GLY A 453 " pdb=" C GLY A 453 " pdb=" N LYS A 454 " pdb=" CA LYS A 454 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA LEU A 749 " pdb=" C LEU A 749 " pdb=" N MET A 750 " pdb=" CA MET A 750 " ideal model delta harmonic sigma weight residual 180.00 154.67 25.33 0 5.00e+00 4.00e-02 2.57e+01 ... (remaining 4413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 1098 0.128 - 0.256: 63 0.256 - 0.384: 2 0.384 - 0.513: 0 0.513 - 0.641: 5 Chirality restraints: 1168 Sorted by residual: chirality pdb=" P DT C 20 " pdb=" OP1 DT C 20 " pdb=" OP2 DT C 20 " pdb=" O5' DT C 20 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" P DG C 17 " pdb=" OP1 DG C 17 " pdb=" OP2 DG C 17 " pdb=" O5' DG C 17 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 8.04e+00 chirality pdb=" P DA C 19 " pdb=" OP1 DA C 19 " pdb=" OP2 DA C 19 " pdb=" O5' DA C 19 " both_signs ideal model delta sigma weight residual True 2.34 -2.90 -0.57 2.00e-01 2.50e+01 7.99e+00 ... (remaining 1165 not shown) Planarity restraints: 1136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 782 " 0.028 2.00e-02 2.50e+03 3.00e-02 1.58e+01 pdb=" CG PHE A 782 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 PHE A 782 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 782 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 782 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 782 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 782 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 823 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C ASN A 823 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN A 823 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU A 824 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 733 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO A 734 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 734 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 734 " -0.036 5.00e-02 4.00e+02 ... (remaining 1133 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2751 2.89 - 3.39: 8655 3.39 - 3.89: 13749 3.89 - 4.40: 15686 4.40 - 4.90: 22488 Nonbonded interactions: 63329 Sorted by model distance: nonbonded pdb=" O PRO A 248 " pdb=" OE1 GLU A 252 " model vdw 2.386 3.040 nonbonded pdb=" O GLU A 399 " pdb=" OE1 GLU A 403 " model vdw 2.392 3.040 nonbonded pdb=" O TYR A 518 " pdb=" OE1 GLN A 522 " model vdw 2.396 3.040 nonbonded pdb=" O LYS A 576 " pdb=" OE1 GLU A 580 " model vdw 2.405 3.040 nonbonded pdb=" O PHE A 782 " pdb=" OE1 GLN A 786 " model vdw 2.407 3.040 ... (remaining 63324 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: 1.630 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.760 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 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 : 0.006 0.068 7618 Z= 0.428 Angle : 1.203 13.340 10573 Z= 0.730 Chirality : 0.074 0.641 1168 Planarity : 0.008 0.091 1136 Dihedral : 22.075 178.929 2970 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 31.08 Ramachandran Plot: Outliers : 0.79 % Allowed : 2.37 % Favored : 96.84 % Rotamer: Outliers : 0.48 % Allowed : 1.27 % Favored : 98.25 % 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: -1.68 (0.29), residues: 760 helix: -0.41 (0.24), residues: 398 sheet: -3.69 (1.63), residues: 10 loop : -1.84 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 792 TYR 0.025 0.003 TYR A 518 PHE 0.070 0.004 PHE A 782 TRP 0.041 0.004 TRP A 287 HIS 0.010 0.001 HIS A 811 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.43 ( 7618) covalent geometry : angle 1.20282 / 0.73 (10573) hydrogen bonds : bond 0.16907 / 10.98 ( 334) hydrogen bonds : angle 7.64786 / 5.58 ( 935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 103 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.6055 (tpt) cc_final: 0.5049 (tpt) REVERT: A 54 MET cc_start: 0.6910 (mtp) cc_final: 0.3851 (mmt) REVERT: A 91 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7705 (pm20) REVERT: A 339 ASN cc_start: 0.9266 (m-40) cc_final: 0.8900 (m110) REVERT: A 443 LEU cc_start: 0.8651 (pp) cc_final: 0.8404 (pp) REVERT: A 847 ASP cc_start: 0.9476 (m-30) cc_final: 0.9103 (p0) outliers start: 3 outliers final: 1 residues processed: 105 average time/residue: 0.1076 time to fit residues: 14.7822 Evaluate side-chains 69 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 67 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 0.9980 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.066225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.048123 restraints weight = 70134.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.050032 restraints weight = 47665.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.051325 restraints weight = 36433.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.052156 restraints weight = 30513.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.052464 restraints weight = 27122.966| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 7618 Z= 0.242 Angle : 0.907 10.755 10573 Z= 0.496 Chirality : 0.053 0.282 1168 Planarity : 0.006 0.042 1136 Dihedral : 27.083 179.563 1528 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 33.07 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.00 % Favored : 89.61 % Rotamer: Outliers : 0.32 % Allowed : 5.88 % Favored : 93.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.62 (0.29), residues: 760 helix: -0.48 (0.24), residues: 414 sheet: -3.93 (0.88), residues: 20 loop : -1.57 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 792 TYR 0.017 0.002 TYR A 44 PHE 0.040 0.003 PHE A 400 TRP 0.019 0.002 TRP A 797 HIS 0.006 0.001 HIS A 799 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.24 ( 7618) covalent geometry : angle 0.90667 / 0.50 (10573) hydrogen bonds : bond 0.08660 / 5.78 ( 334) hydrogen bonds : angle 5.81377 / 4.22 ( 935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7300 (mtp) cc_final: 0.4322 (mmm) REVERT: A 141 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.8940 (tp) REVERT: A 847 ASP cc_start: 0.9513 (m-30) cc_final: 0.9117 (p0) outliers start: 2 outliers final: 0 residues processed: 84 average time/residue: 0.0883 time to fit residues: 10.0237 Evaluate side-chains 61 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 79 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 34 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 65 optimal weight: 20.0000 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 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 = 0.3675 r_free = 0.3675 target = 0.079830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.068582 restraints weight = 89321.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.070278 restraints weight = 52422.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.071356 restraints weight = 35733.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.072055 restraints weight = 27180.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.072476 restraints weight = 22492.402| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 7618 Z= 0.278 Angle : 0.911 9.419 10573 Z= 0.503 Chirality : 0.055 0.311 1168 Planarity : 0.006 0.076 1136 Dihedral : 27.118 177.353 1528 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 40.04 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.08 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % 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: -1.92 (0.29), residues: 760 helix: -0.71 (0.23), residues: 409 sheet: -3.49 (0.74), residues: 36 loop : -1.63 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG A 394 TYR 0.017 0.002 TYR A 739 PHE 0.053 0.004 PHE A 400 TRP 0.017 0.002 TRP A 201 HIS 0.004 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.28 ( 7618) covalent geometry : angle 0.91090 / 0.50 (10573) hydrogen bonds : bond 0.09214 / 6.15 ( 334) hydrogen bonds : angle 6.00954 / 4.32 ( 935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7249 (tpt) cc_final: 0.6542 (tpt) REVERT: A 193 LYS cc_start: 0.9527 (pptt) cc_final: 0.9120 (tptp) REVERT: A 733 PHE cc_start: 0.9072 (p90) cc_final: 0.8808 (p90) REVERT: A 847 ASP cc_start: 0.9529 (m-30) cc_final: 0.9152 (p0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0893 time to fit residues: 10.1444 Evaluate side-chains 59 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 70 optimal weight: 40.0000 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 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 = 0.3685 r_free = 0.3685 target = 0.080220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.068810 restraints weight = 90439.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.070556 restraints weight = 52313.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.071667 restraints weight = 35398.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.072390 restraints weight = 26784.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.072797 restraints weight = 22074.986| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7618 Z= 0.218 Angle : 0.858 12.158 10573 Z= 0.466 Chirality : 0.053 0.339 1168 Planarity : 0.006 0.066 1136 Dihedral : 27.139 175.282 1528 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 36.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.66 % Favored : 88.95 % Rotamer: Outliers : 0.16 % Allowed : 5.56 % Favored : 94.28 % 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: -1.93 (0.29), residues: 760 helix: -0.71 (0.24), residues: 404 sheet: -3.65 (0.69), residues: 38 loop : -1.59 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 155 TYR 0.016 0.002 TYR A 739 PHE 0.038 0.003 PHE A 400 TRP 0.039 0.002 TRP A 620 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.22 ( 7618) covalent geometry : angle 0.85785 / 0.47 (10573) hydrogen bonds : bond 0.07271 / 4.94 ( 334) hydrogen bonds : angle 5.83824 / 4.19 ( 935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.9526 (pptt) cc_final: 0.9105 (tptp) REVERT: A 666 MET cc_start: 0.6609 (mmm) cc_final: 0.6290 (tpt) REVERT: A 847 ASP cc_start: 0.9508 (m-30) cc_final: 0.9126 (p0) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.0901 time to fit residues: 10.0001 Evaluate side-chains 55 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 4 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.054058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.038502 restraints weight = 72668.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.040055 restraints weight = 49068.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.041052 restraints weight = 38099.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.041737 restraints weight = 32506.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.042155 restraints weight = 29087.387| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 7618 Z= 0.277 Angle : 0.890 9.551 10573 Z= 0.490 Chirality : 0.054 0.340 1168 Planarity : 0.006 0.063 1136 Dihedral : 27.103 175.374 1528 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 44.66 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.26 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.18 (0.29), residues: 760 helix: -0.81 (0.23), residues: 407 sheet: -4.04 (0.57), residues: 46 loop : -1.74 (0.37), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 478 TYR 0.016 0.002 TYR A 739 PHE 0.030 0.003 PHE A 849 TRP 0.021 0.002 TRP A 620 HIS 0.017 0.002 HIS A 784 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.28 ( 7618) covalent geometry : angle 0.89022 / 0.49 (10573) hydrogen bonds : bond 0.09349 / 6.31 ( 334) hydrogen bonds : angle 5.99323 / 4.30 ( 935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8115 (tpt) cc_final: 0.7520 (tpt) REVERT: A 193 LYS cc_start: 0.9493 (pptt) cc_final: 0.9079 (tptp) REVERT: A 666 MET cc_start: 0.6908 (mmm) cc_final: 0.6441 (tpp) REVERT: A 800 GLU cc_start: 0.9116 (tp30) cc_final: 0.8817 (mm-30) REVERT: A 847 ASP cc_start: 0.9579 (m-30) cc_final: 0.9268 (p0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0917 time to fit residues: 9.5487 Evaluate side-chains 52 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 5 optimal weight: 8.9990 chunk 80 optimal weight: 30.0000 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 8 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 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 = 0.3448 r_free = 0.3448 target = 0.056423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.040745 restraints weight = 72488.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.042301 restraints weight = 50939.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.043300 restraints weight = 40083.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.043975 restraints weight = 34324.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.044415 restraints weight = 30831.381| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 7618 Z= 0.206 Angle : 0.864 9.680 10573 Z= 0.469 Chirality : 0.053 0.350 1168 Planarity : 0.005 0.063 1136 Dihedral : 27.108 174.317 1528 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 36.27 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.66 % Favored : 88.95 % Rotamer: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.07 (0.29), residues: 760 helix: -0.74 (0.23), residues: 409 sheet: -3.94 (0.69), residues: 38 loop : -1.75 (0.36), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 84 TYR 0.018 0.002 TYR A 739 PHE 0.031 0.002 PHE A 849 TRP 0.012 0.002 TRP A 502 HIS 0.008 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.21 ( 7618) covalent geometry : angle 0.86389 / 0.47 (10573) hydrogen bonds : bond 0.06758 / 4.61 ( 334) hydrogen bonds : angle 5.79791 / 4.18 ( 935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.9512 (pptt) cc_final: 0.9084 (tptp) REVERT: A 313 MET cc_start: 0.5399 (tpp) cc_final: 0.4985 (tpp) REVERT: A 666 MET cc_start: 0.7104 (mmm) cc_final: 0.6591 (tpp) REVERT: A 847 ASP cc_start: 0.9544 (m-30) cc_final: 0.9196 (p0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0873 time to fit residues: 9.3816 Evaluate side-chains 54 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 45 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 78 optimal weight: 20.0000 chunk 23 optimal weight: 0.0370 chunk 66 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 32 optimal weight: 0.0030 chunk 36 optimal weight: 20.0000 overall best weight: 1.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 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 = 0.3703 r_free = 0.3703 target = 0.080627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.069770 restraints weight = 89336.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.071503 restraints weight = 51621.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.072579 restraints weight = 34821.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.073274 restraints weight = 26083.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.073729 restraints weight = 21504.152| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7618 Z= 0.181 Angle : 0.835 8.560 10573 Z= 0.455 Chirality : 0.052 0.330 1168 Planarity : 0.005 0.061 1136 Dihedral : 27.115 174.697 1528 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 31.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.39 % Favored : 89.21 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: -1.95 (0.30), residues: 760 helix: -0.68 (0.24), residues: 409 sheet: -3.87 (0.92), residues: 22 loop : -1.83 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 34 TYR 0.014 0.001 TYR A 739 PHE 0.029 0.002 PHE A 849 TRP 0.011 0.001 TRP A 502 HIS 0.008 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 ( 7618) covalent geometry : angle 0.83549 / 0.45 (10573) hydrogen bonds : bond 0.05738 / 3.90 ( 334) hydrogen bonds : angle 5.70646 / 4.11 ( 935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 LYS cc_start: 0.9561 (pptt) cc_final: 0.9145 (tptp) REVERT: A 313 MET cc_start: 0.4826 (tpp) cc_final: 0.4567 (tpp) REVERT: A 666 MET cc_start: 0.7121 (mmm) cc_final: 0.6598 (tpp) REVERT: A 800 GLU cc_start: 0.9060 (tp30) cc_final: 0.8823 (mm-30) REVERT: A 847 ASP cc_start: 0.9514 (m-30) cc_final: 0.9188 (p0) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0846 time to fit residues: 9.4135 Evaluate side-chains 56 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 55 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 58 optimal weight: 0.0010 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 0.0670 overall best weight: 2.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 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 = 0.3692 r_free = 0.3692 target = 0.080162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.069311 restraints weight = 89795.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.071004 restraints weight = 51338.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.072130 restraints weight = 34854.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.072814 restraints weight = 26136.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.073281 restraints weight = 21483.958| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7618 Z= 0.180 Angle : 0.826 8.572 10573 Z= 0.451 Chirality : 0.051 0.325 1168 Planarity : 0.005 0.084 1136 Dihedral : 27.080 175.287 1528 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 32.64 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.26 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -1.92 (0.29), residues: 760 helix: -0.65 (0.24), residues: 409 sheet: -3.90 (0.89), residues: 22 loop : -1.81 (0.36), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 756 TYR 0.012 0.001 TYR A 739 PHE 0.028 0.002 PHE A 849 TRP 0.013 0.002 TRP A 502 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 ( 7618) covalent geometry : angle 0.82582 / 0.45 (10573) hydrogen bonds : bond 0.05965 / 4.04 ( 334) hydrogen bonds : angle 5.67441 / 4.07 ( 935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.8146 (tpt) cc_final: 0.7692 (tpt) REVERT: A 193 LYS cc_start: 0.9560 (pptt) cc_final: 0.9147 (tptp) REVERT: A 313 MET cc_start: 0.5357 (tpp) cc_final: 0.5104 (tpp) REVERT: A 666 MET cc_start: 0.7091 (mmm) cc_final: 0.6530 (tpp) REVERT: A 800 GLU cc_start: 0.9061 (tp30) cc_final: 0.8840 (mm-30) REVERT: A 847 ASP cc_start: 0.9515 (m-30) cc_final: 0.9202 (p0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0884 time to fit residues: 9.3487 Evaluate side-chains 54 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 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 = 0.3682 r_free = 0.3682 target = 0.079613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.068628 restraints weight = 87795.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.070312 restraints weight = 51184.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.071380 restraints weight = 34984.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.072037 restraints weight = 26595.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.072560 restraints weight = 22084.774| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7618 Z= 0.186 Angle : 0.824 10.692 10573 Z= 0.448 Chirality : 0.051 0.328 1168 Planarity : 0.005 0.064 1136 Dihedral : 27.050 175.310 1528 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 31.58 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.26 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.86 (0.30), residues: 760 helix: -0.57 (0.24), residues: 408 sheet: -4.02 (0.88), residues: 22 loop : -1.80 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 155 TYR 0.024 0.002 TYR A 739 PHE 0.028 0.002 PHE A 849 TRP 0.014 0.002 TRP A 502 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 ( 7618) covalent geometry : angle 0.82386 / 0.45 (10573) hydrogen bonds : bond 0.06054 / 4.11 ( 334) hydrogen bonds : angle 5.57767 / 4.01 ( 935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7732 (tpt) cc_final: 0.6600 (tpt) REVERT: A 193 LYS cc_start: 0.9582 (pptt) cc_final: 0.9163 (tptp) REVERT: A 666 MET cc_start: 0.7115 (mmm) cc_final: 0.6572 (tpp) REVERT: A 847 ASP cc_start: 0.9506 (m-30) cc_final: 0.9178 (p0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0910 time to fit residues: 9.4709 Evaluate side-chains 55 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 68 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 14 optimal weight: 20.0000 chunk 73 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 62 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 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 = 0.3695 r_free = 0.3695 target = 0.080301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.069337 restraints weight = 87121.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.071013 restraints weight = 50627.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.072084 restraints weight = 34574.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.072781 restraints weight = 26379.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.073272 restraints weight = 21663.887| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7618 Z= 0.177 Angle : 0.833 10.508 10573 Z= 0.449 Chirality : 0.051 0.330 1168 Planarity : 0.005 0.063 1136 Dihedral : 27.063 175.063 1528 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 30.37 Ramachandran Plot: Outliers : 0.53 % Allowed : 10.13 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.30), residues: 760 helix: -0.58 (0.24), residues: 409 sheet: -4.17 (0.64), residues: 36 loop : -1.72 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 746 TYR 0.015 0.002 TYR A 250 PHE 0.028 0.002 PHE A 849 TRP 0.017 0.002 TRP A 502 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 ( 7618) covalent geometry : angle 0.83344 / 0.45 (10573) hydrogen bonds : bond 0.05721 / 3.87 ( 334) hydrogen bonds : angle 5.60191 / 4.00 ( 935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7627 (tpt) cc_final: 0.6680 (tpt) REVERT: A 193 LYS cc_start: 0.9585 (pptt) cc_final: 0.9156 (tptp) REVERT: A 666 MET cc_start: 0.7137 (mmm) cc_final: 0.6572 (tpp) REVERT: A 677 MET cc_start: 0.9526 (mmp) cc_final: 0.9309 (mmm) REVERT: A 847 ASP cc_start: 0.9500 (m-30) cc_final: 0.9172 (p0) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0842 time to fit residues: 8.8937 Evaluate side-chains 55 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 63 optimal weight: 0.0970 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 781 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 852 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 = 0.3675 r_free = 0.3675 target = 0.079119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.068283 restraints weight = 88199.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.069921 restraints weight = 51109.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.070985 restraints weight = 35076.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.071644 restraints weight = 26618.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.072129 restraints weight = 22261.808| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7618 Z= 0.187 Angle : 0.844 12.991 10573 Z= 0.452 Chirality : 0.051 0.329 1168 Planarity : 0.005 0.067 1136 Dihedral : 27.057 175.928 1528 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 32.93 Ramachandran Plot: Outliers : 0.53 % Allowed : 9.61 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: -1.80 (0.30), residues: 760 helix: -0.46 (0.24), residues: 408 sheet: -4.11 (0.87), residues: 22 loop : -1.87 (0.36), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 746 TYR 0.018 0.002 TYR A 739 PHE 0.028 0.002 PHE A 849 TRP 0.017 0.002 TRP A 502 HIS 0.007 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 ( 7618) covalent geometry : angle 0.84371 / 0.45 (10573) hydrogen bonds : bond 0.06340 / 4.28 ( 334) hydrogen bonds : angle 5.59130 / 4.02 ( 935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1430.96 seconds wall clock time: 25 minutes 45.99 seconds (1545.99 seconds total)